<lots of words>
I was dead certain it worked how I described it, so I tested it just now and proved....
Myself wrong.
You are 100% correct here.
Although I think I might have figured out where the supplies went.
If you do the tutorial without doing anything special, all the repairs you do while travelling means when you get back to Ancyra will all the ships it looks like this:
And when you fill up your crew, the repair bill looks like this:
21 supplies.
But when you mothball a ship it gets it's CR set to zero, so when you pitch up at Ancyra it looks like this:
And when you re-activate the ships and fill up on crew the repair bill looks like this:
83 supplies.
So by mothballing your ships, you essentially throw away all the repair recovery, and whatever CR recovery the reduced crew can manage during the journey over.
The supply situation after returning from Tetra
With mothballing:
And without mothballing:
(Also 50 supplies confirmed.)
The difference is only 11 supplies between them.
And yet the complete repair and recovery of those ships from mothballed costs 62 supplies more than if you'd just leave the ships undercrewed on the way back.
That's where the supplies have gone.
This doesn't address the whole 'invisible time limit' thing though.