You could also transplant the auto as you would a photo as long as its done no later than week 3. I've transplanted during week 4 before but it isn't recommended.
Just transplanted these autos last night with no issues. Day 27 from sprout. I think you'll be fine transplanting them or letting them grow through the bag. If you are worried, you could probably slice the sides of the bag several times before dropping it in more soil.
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.