I'll try to explain a bit better I guess...
if he was on the PUP he'd be unable to practice. by taking him off the PUP they can have him practice and see if he can work through any presumed sorenss, weakness, issue that has not allowed him to come back. 9 months is a long time after any shoulder surgery. to be honest he should have been throwing at least 3 months ago. if he can't work through his stuff they IR him and he has surgery. if he can, great, maybe he's back by week 5 or 6. I'm just sharing my opinion and take it for what it's worth. I was right last time this happened with Peyton manning and everyone gave me crap before he had another surgery. go look in the gronk thread and you'll see how much crap I got for predicting what I did. only been 1 game but I look more correct than not on that one.
I'm sure I could be wrong and they're just being precautious... but it seems more likely, to me, something is wrong rather than everything is fine and they're being cautious for strength