...Flat out, a player fleet orbiting a player-owned colony should not use supplies (except for repairs or regenerating CR). Nor should it charge the player for crew or marine upkeep costs.
Realism has nothing to do with it. This is a game design decision to remove the otherwise very present incentive for the player to just stuff 98% of their fleet into storage and idle in a single cheap frigate. This is something I've done, and it always annoys me to have to pull stuff back out and re-set officers.
Now, in general, I don't use this for a "skip time while waiting on passive income"; I use this for "I need to stick around in this area to deal with X incoming problem" or to wait until I can actually install a colony item (since you can't just drop those in storage and install them remotely later). And particularly if I set up a colony relatively early in the game, I may have cause to conserve supplies while I wait.
And even late game, if I'm waiting on something, the temptation is there to just drop down to that single frigate to save some credits. Not usually worth the fuss at that point, but proper game design should remove the temptation.
(I mean, the other way to remove the temptation would be to have ships/crew in storage still draw their full costs. But that doesn't sound like any fun at all.)