Was body rejection even a possibility?
I think that yes, body rejection was possible, but we only ended up seeing situations where it hadn't happened. 

Barry was number 65 (or something). I think it's possible some of the other 64 failed in their soul transpositions.

We did see Al loose consciousness a couple times - I assume that's when his armour was rejecting his soul.

I think that Alphonse was protected by plot, though.