Knowing more of the car's history, I'd have to say that it's pretty unlikely that the
cooling system could be clogged by stop leak.
If you had it checked the first time it overheated and a cracked head didn't show
up then, I'd say you should be okay.
It would take quite a bit of stop leak to break loose and clog up the system which
would mean that the first time it was checked, you would have most likely found
a cracked head at that time.
Still, it could be a possibility however remote it might be.
It still concerns me that the car doesn't hold all the antifreeze that it did before...
Sometimes air can get trapped in the cooling system, especially after a full system
flush, but I've never seen one where you could only get 1/3 of the coolant back in.
On some cars there are bleed valves to release the trapped air and fully fill the system.
Might want to check into that to make sure it was done.
Scott