I've been using the grow bags for a few years, they're economical and work great.
As others have mentioned, there's no reason whatsoever an auto can't be transplanted just like a photoperiod.
I generally cut off the bag. I've never noticed any slowdown at all with transplanting; if anything growth seems to increase once the roots are unshackled. I usually see roots poking through my 2 gal fabric pots in 3-5 days after transplanting.