Your proofreader felt disturbed because there may be some inconsistencies in your story.
I'll point my finger against the fact that you changed some country names. This - per se - is not a problem, but it does depend on a lot of different factors. Let's review.
In an alternate-history story, it's totally legitimate changing some details in a way that suit us. The readers will accepts this changes if they recognize they are needed for an interesting narrative. For example, if the russian revolution never occurred - or occurred later - the outline of the war would be already pretty much different.
So, the question is: are you changing names because your countries are different?
Let's say that in this alternate setup Germany is, instead, called Svervegia. That's alright, since this is alternative history; but by changing the name, we are signaling the reader that this country is not an exact copy of '900 Germany.
So, what is different? What is the root cause of this change in the country's own name? Are the borders the same? Is the culture the same? In what aspects this country mimics the one we historically know, and in what it differs?
The readers will be asking those questions, and expect suitable answers in your novel (at least, they will expect you to hint at answers). Alternate history gives you the power to make all the changes you want - but remember that only a part of those changes will be excused by suspension of disbelief.
If your main objective is "I want to write an alt-history WWI novel were dragons exists" the readers will accept the quirk, but they will expect to see how this impacts the whole enviroment.
In pretty much the same way, if your objective is "I want to write an alt-history WWI novel were the main countries are different" is totally fine to change names: but you will need to explain what those differences are.
Alternative History vs Historical Accuracy
I'm afraid you have stumbled upon two pretty incompatible concept.
The more your history is alternative, the less it will be accurate.
There is no way around it.
Of course, once you decide the main "quirk" of you alternative history, you can decide how it changes every event in a cause-effect chain in the most "likely" way. The resulting history won't be 100% accurate anymore, but it will make a realistic, "likely", hopefully interesting) alternative.
Some things of course won't be affected by your changes and you can still be "accurate" on them. Yet, I suspect that the point is not about being accurate, is about being credible.
Then again, why
I'm adding this paragraph since I'm a little uncertain on the whole premise of your question. You stated:
Yet, I wish not to convey ideas of the time, like how which country was bad, which country was good.
As I wanted to take some distance from our world, I had the idea to change some names like country names.
There is no unbiased opinion about "which country was bad". Any historian would tell you that there were good and bad aspects in each and every country. Being a century later, we can examine things more objectively and decide which country was probably better for our modern world standards, but people at the time had different thoughs.
Your mentioned that your characters aren't patriots, so you're free to give them complex opinions on the respective countries. They will have insights on the good points and on the bad points. And being characters, they're free to be wrong: their opinion is not - and should not - be your opinion as a narrator/writer.
You don't need to change country names without a good reason to do so. If you want to give insights about the involved countries, you already have ways to do that from each character PoV: all the better since they are from opposing factions. Maybe you can use this to show how each one will have different opinions on the other. Some of those will be wrong. Some of those will be correct. Some will be propaganda.
So, being coherent and gaining the reader trust
In the end, a rose by any other name would smell as sweet, as Shakespear said, but if we're talking about a rose, the most straightforward way is calling it a rose.
Changed names will mean substantial changes in everything else too. Your audience will expect this statement to be correct. If it isn't, or it feels like you're using nonces without a reason backing it up, your readers will feel cheated or upset.
If there are no changes, you're better off using real names and adding "distance" through other means; after all, it's better to focus the readers attention on the true elements in your novel that are "alternate history".