If the flag was called 'Requires Maintenance & Naval Shipyard' vs 'Doesn't Require Maintenance & Naval Shipyard', would that be easier to accept without suspension of disbelief?
Calling it a convenience feature is not exactly the best wording on my part. What I meant was that it is exactly as you said a choice about gameplay and micromanagement, and anchored entirely on game mechanic. The only in-world justification is high-maintenance vs low-maintenance, and for simplicity's sake there is no further graduation.
I very welcome the addition of commercial magazines and maintenance supply storage, which had been a weird point of "Why does a magazine cause my engine to fail" Similarly I very much like the new structural hull, that offers a clear choice between orbital platform and ship, not needing an orbital habitat for the completely different purpose of building it by construction factories.
What I meant for the most part, once you define a role, you automatically define military or commercial flag. Any decent sensors, any weapons, any high powered engine triggers it.
My suspension of disbelief is not threatened by the exact wording, but specifically by heavily armored commercial-flagged drop ships, since there are many systems I might reasonably add which suddenly make it military flagged.
Classifying drop modules as military modules would resolve the issue, but might require some other adjustment to not make landings impossibly hard. Limiting the armor to 1 layer would also do it.
I am very worried that the benefits of no maintenance will completely outclass any other possible drop ship design. There is every incentive not to experiment with adding weapons, adding shields, better sensors, because it would all make it a lot more expensive by breaking commercial status. That feels just sad. Yes, pure armor+drop module designs will preform good, and likely better than many of the complicated designs, but they at least won't be much worse, and thus people will experiment with them, but the expense of the shipyards and maintenance will block most of that off.