That sounds like a very annoying system for anyone with even vague OCD tenancies.
Slightly off topic, but. . yes. Diagnosed and all, and I assure you it is a pain in the behind. People who 'just like things neat' simply don't understand. It's like being extremely anxious and nervous over what others don't even realise exists and objectively doesn't deserve that response.
The super giant sounds fun, aha. Thanks for the heads up. Also unfortunately for your other idea, the asteroids are all orbiting the main star so that's several hundred manual adjustments. I'll just sit back with my SM mode and call it even, lol.
In regards to NPRs I would make a relatively educated guess that it wouldn't do anything negative at all.
It's clear even in player interactions that ships don't go to the destination's rendezvous location but rather constantly head directly towards it and make adjustments to the new orbited location each tick. Running out of fuel or otherwise moving it too far away for their units to reach at the time wouldn't have any direct effect either, as there's a catch where any out of fuel NPR ship can always (but only) move towards a valid refueling spot at full speed.
Further, after thinking about it, ships automatically move every time a body location is updated if they're orbiting. The only time they don't is if being overhauled by a station, then they get locked in place while the station orbits (presuming that the station is orbiting a body itself, as is required. ) That's actually a bug, too, already reported.