I would say that you can't assume that the skinnyness is due to under feeding - as pet shops quite often over feed on pellets/bitty foods so they might have runny poos and bads tummies, they still put on weight because of fat contents, and mites, ringworm etc can become rife without much notice or proper treatment so they go off food, which I would if I was stuck in a tiny pen with no attention!
I'd say you could judge from a couple of visits on different days, one in the morning and one later on in the day on a different day, so you can judge the levels of food there including hay/straw levels, but also as to weather they have a hiding place because if they don't have one, being scared can also cause problems.
I'm glad to hear your guy has fattened up since he's been with you, and good luck with your investigations..... x