Some thoughts on this:

The game does not visually accommodate for this. The windows on crew quarters always align "horizontally", as do engines, thus they always mismatch. One can of course work around with blank hull exterior and manually placed placebo windows.

Also the game does seem to imply use of artificial gravity/inertia, otherwise your ships would either not be able to compete with AI ships with regards to acceleration and turning rates, or your squishy crew would soon get splattered across the floor (whichever direction the current "floor" would be).

So while one might build "realistoid" ships, in my opinion it just doesn't really make sense in Avorion. Just accept that it is BattleStarTrekWars, and run with the theme.

The only game that I know of that accurately models acceleration is "Children of a Dead Earth" with more realistic ships and space combat in general... but of course, that's just catering to one very specific game aspect.

Edit: Regarding fun, immersion, and retention, I can't help but note that I have spent hundreds of hours in Avorion, and only a few in CoaDE...