First of all, I agree that there's no actual bug, i.e. something causing problems with gameplay. However...
The hidden compartments automatically get used they way you'd want them to.
I see. So say I have a Tarsus, and buy 2 hidden compartments, and then 50 units of grain, when I had my compartment back in version 4.7 (haven't used them since) my cargo manifest would say 48 units grain in cargo +2 in hidden.
That imho shouldn't happen. The hidden compartments should never be used for legal cargo, unless there's no more free space in non-hidden cargo units.
Yes, as soon as you actually need the hidden ones, AS will properly reorganize the cargo. But I still think this would be confusing.
I gotta say that I'm surprised I never noticed this. But I'm also too lazy to test it right now, sorry.

-- Cort