I've a little experience writing sci-fi, so take my advice with at least half a pinch of salt, but here's my way of looking at it:
he figures out how to chemically produce water from shuttle fuel and grows plants for food from the seeds that his crashed shuttle was carrying.
Sci-fi explains how things are done with two motives: to make it seem plausible, and to introduce an important premise for the plot. As an example of the latter, the Doctor Who episode The Waters of Mars explains how Martian geography provided the base with a water supply, but it turns out, despite purification efforts, to have an unexpected alien contaminant that causes the plot. Therefore, there's no reason to explain such former-motive minutiae as what contaminants they would expect (such as perchlorates, not that I know much about Martian polar caps), how the water is melted and pumped against gravity, and so on.
I think your problem may be you are too verbose with regards to the plausibility motive. If you're worried, "Luckily, I knew how to make water from rocket fuel" sounds too much like convenience to people who don't know water can be made from hydrazine, you can still achieve your goals with, "Luckily, the rocket had enough hydrazine left over to make water." That one sentence is all it takes to cover hydrogenesis, it only has one word in it, and a few seconds of Googling will make the reader realize, "oh, so that's a thing in fuel you can turn into water, cool". You can do something similar with growing food from seeds: the only real challenge is how you productively use Martian soil, but it'll come down to a reaction with one reagent or product you can name fast before you move on.
The mechanism is unimportant; its requirements are all you need to mention. The obvious exception is if you want to explain that A was done instead of B, which would also work, because it has advantage C. There are works that take the time to do that, quite successfully, in part because of niche readers.
characters use science-specific lingo or "technobabble" in dialogue to explain things that are happening on the ship, i.e. referencing the concept of ion acceleration to explain how the ship's ion propulsion works and why it went wrong in the protagonist's crashed shuttle (I referenced this NASA webpage).
Please tell me you didn't put a hyperlink in your novel! Apart from practical reasons readers either can't or won't read it, or may even not know it's there, it means you've not narrowed down what they have to read. "All of it" sends the wrong message. The right message is the rocket uses an ion engine because it makes the ship lighter, so it's just more practical. In theory, that one fact is all you need anyone to say. In practice, why would they say it, when they're all spacefarers who know it? I suppose you could work around that with the token ignoramus who needs it explained, or the ion engine salesman who mentions these new ships are the most lightweight ones on the market; I'll let you decide which is least cliché to insert.
The protagonist is also a scientist and references biology and chemistry concepts frequently in his inner monologue.
In my opinion, this would also benefit from the light-touch approach I describe above. How you word it depends on their personality. Autistic or not, they might use a common speech style, e.g. "You've gotta work out half the day or this micrograv'll waste you away." Might. I don't know why you made the character autistic, but it presents an opportunity you likely already picked up on as a writer: part of their character development can be gradually improving the way they talk about things to other people so they won't feel overwhelmed, while his own thought processes either don't change in this way or do so more slowly. (Admittedly, the isolation in the plot limits the fraction of the story in which talking to other people comes up, but every conversation that survives must be made to count.)
not everyone will understand the chemistry concepts that the protagonist explains to the reader through his internal monologue, such as the chemical reaction he uses to make water from jet fuel. I worry that some parts are coming across as too information-dense and want to make it easier on the reader as a whole.
As I said, you can explain very succinctly. There is a way to make water from hydrazine. I can already visualize a pre-isolation scene where your character explains it in more detail, only for an exasperated person to snap they don't care how it's done. If your protagonist's first explanation of something in the story is the only one that overdoes it, you'll benefit in several ways:
- Readers will be happy most if not all of the time;
- "Do you know your onions?" sci-fi readers will be convinced you know them fast;
- Your plot will dovetail nicely with your characterization. Getting snapped at like that will have an effect on your character that's bound to be obvious as it unfolds.
You know what? I owe you an apology. I keep rewriting your story. Let's make that a full pinch of salt now.
I've been trying to solve this by making the explanation more casual and conversational, and avoiding using specific terms, i.e. instead of using the word "ion," the engineer could just say "charged particles." But I'm not sure that is the right approach, hence my question today.
What's charge? What's a particle? Who can answer both questions, but was sleeping when their science teacher said what an ion was? How annoyed will "smart" readers be that you seem to think every charged particle is an ion? (I suppose you could argue an electron is a mono-negative anion of neutronium-0, but no!) You get the worst of both words with that example. You can afford one "dammit I'll have to Google that" word every 2,000 or so - just use it, then move on. As I've said, the problem is how long you explore why ion thrusters are great, not that you mention ions exist.
What is the best way to avoid or mitigate dense "technobabble" and scientific lingo in a science fiction setting, and make it easier on the reader in general?
The only response I can give consistent with the above advice is to use it a bit, but use it in a very different way from the one your beta readers have detected.
How should I explain a possibly unfamiliar science concept to a general reader in a way that's engaging to read?
OK, that's the one situation I've not adequately addressed so far. Let's take an example: growing seeds in the Martian soil. As noted here, the nutrients aren't the hard part. The hard part is (i) not having much of what else plants want - light, heat, carbon dioxide and (ii) having to leach out poisonous perchlorates. You can explain one or both of these, and you can go into a lot of detail or not very much. But it needs to be a level of detail that fits the scene. If it were a dialogue, you can imagine:
"How are you gonna make fertilizer?"
"That's not even the problem."
"What is, then?"
"The soil's poisoned. We can fix it, but it wastes a lot of power."
The plot, personalities etc. drive the exposition. In your case, though, it wouldn't be in dialogue. There's still such a thing as fitting the scene, though, because an inner monologue will still contain a certain sequence of thoughts, just like dialogue does. So you might have something like:
"The soil seemed all right when I looked at it. Well, the scan found slightly more perchlorate poisoning than I'd planned on. Oh, well, I could fix that, it just meant sparing a bit more power for water treatment."
Again, my point isn't that that's literally what you should write. It might not even suit your character. The point is to think about what our explanations are actually for. My null hypothesis is that their purpose is adequately suited by this kind of succinct aside. It might be a wrong hypothesis, but I suggest starting in this small way, then building on it if you decide it's insufficient.