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So, Aeronautica Imperialis, can you give these flyers a custom regiment? I know you will not gain the ability to use Regiment Doctrines.

I'm not sure what you're asking.

The 'Regiment' attributes in the IG codex will state which models they affect, using keywords such as <INFANTRY>, <TANK> etc.

Generally speaking, if the Forgeworld Indexes feature the same keywords and can be added to a normal Imperial Guard force, they will gain the 'Regiment' trait in question. However, you're talking about a custom regiment so I don't know what you mean. Are you creating your own rules, or do you just want to paint them up a certain way?

Not really understanding the question.

So certain strategems work with specific regiment keywords, so while not gaining regiment doctrines, it would allow certain strategems to work with them. It feels like they just left the flyers out in the wind (see what I did there). They dont belong to anything.

<Aeronautica Imperialis> is their <REGIMENT> so no you cannot replace <Aeronautica Imperialis> with <REGIMENT> of your choice. Unless there is a weird datsheet that has both?

None of the Astra Copywritum flyers have <REGIMENT>.

You can say they are in your regiment, you can paint them as if they were - but the rules give you no way to play them as a part of the regiment.

And the fluff generally says that the AM is not allowed its own airpower anyway - you can blame Horus for that one!

Fluff-wise, AM's structure is supposed to mimic the generic real-world army structure

What [Astra Militarum] is to [Aeronautica Imperialis] is what Army is to Airforce

Each have corresponding "officers" that benefit different branch of the armed forces.

How the AM rules are structured is that you cannot have commander of branch 1 'command' the members of a branch 2.