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I'm writing a short story with androids and cybernetically enhanced humans who have access to neural interfaces. Essentially, they open up some kind of computer terminal, but it's via internal sensors connected directly to their brains, rather than eyes and fingers.

When the characters are viewing the terminal, I can just describe what they're seeing like they're viewing it with their real eyes rather than their mind's eye. But when they interact with the terminal, I want it to be clear the action is neural, not externally physical.

For thoughts, I've been using a combination of narrative thought without special formatting, and italics for quoted thoughts. It's clear and simple and I've seen a number of writers doing the same. Grammar Girl seems to agree it's acceptable.

She wondered if there had been a vote... Not like the mechanicals to name something on a whim.

The first is a paraphrase of an abstract thought, while the second is a specific, word-by-word thought in her head.

From this, my first idea was to format neural actions in italics, like thoughts. But thoughts and neural actions aren't exactly the same.

A few sub-menus later, she pushed the option to flood her body with a kind of tranquilizer.

I've seen this kind of format before, but I'm not sure it has the effect I'm going for. Instead of describing an abstract action, it's almost emphasizing the action. "Typing on a keyboard" is ultimately a short paraphrase for trillions of chemical signals doing their magic inside my brain, so I could just consider neural actions the same way. Alternately, I could explicitly specify it as a neural action.

A few sub-menus later, she activated the neural command to flood...
A few sub-menus later, she activated the option to flood...

The first works, but is needlessly wordy. The second one seems ok, but it's also kind of generic. If I wrote that some guy "activated the door knob" and "activated the steering wheel" it would seem weird and get boring.

Compare "his fingers danced across the backlit keys" to "a slow, steady rhythm echoed through the room as his fingers poked and prodded at the keyboard". I'd rather have the liberty to utilize different verbs depending on the context to make the neural link seem like a real object, but make it clear the verbs are metaphors for physical behavior, not literal physical actions. For example, "she nudged the option" would have a very different contextual implication than "she pushed the option" or "she slammed the link closed with the full force of her fury" even if the underlying circuitry would have the same behavior in all three cases.

An alternate method would be to invent technical jargon, like how we "click" the mouse or "scroll" down the page. In a real scenario, such jargon would undoubtedly form. But I think taking the time to describe a dozen jargon terms in a short story would be counter-productive when I can just use words people already understand. Also, I find that such jargon in TV shows and so forth often seems fake or quaint rather than immersive.

Is there any kind of consensus or precedence for this type of formatting? Or is it more of a "pick something and stick with it" kind of thing? Or is it uncommon enough that nobody cares?

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I'm not aware of any particular consensus, so I think you should pick what works for you. I like the idea that you can nudge, push, or slam an option and each one means something different (even though the electronic action is the same). If the personality performing the action has sentience and intelligence, and particularly emotion, then those differences of expression will exist in whatever medium they act in.

The Star Trek TOS novel Memory Prime has several lengthy passages which take place in computer memory describing the interactions of artificial and natural intelligences (including Spock at one point). You might want to take a look at how the Reeves-Stevenses handled the issue.

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