I believe my transplants grow better root structures. I've damage 1 seedling out of 100+. For me, its a matter of space and timing when running multiple strains. Often my transplants get moved to bigger pots the day after I chop the finished plants. Sometimes, the same day. The last few months there have constantly been seedlings and clones in my veg cab.
Its whatever works for each of us, but I've proven beyond doubt that most autos transplant well.