I know you can't really do much [low] stress training on them [autoflowers].
You can do it, just with limited veg time and short overall plant height, its not going to be as effective as with conventional plants.
If height is a potential problem for you, I'd definitely consider bending/training as an option to keep plants short. Also consider wide-low pots to reduce overall height. Lower volume pots also typically mean smaller overall plants, though size will still be mostly strain dependent with autos.
It "could" work, so long as you understand that
a. Topping autos generally decreases (not increases) their yield, and
b. Short bushy auto structure may not be optimal for SCROG.
If you have to sacrifice yield so as not to burn your plants, that's a perfectly reasonable tradeoff, I think.
I think it could but I am not too sure. Should I just let it do its own thing?
Impossible to answer this without knowing how the plants grow in your particular setup.
If your plant wants to stay short, let it. If not, don't let it.
If you're using one of those super-short dwarf auto strains, two feet may be enough vertical space.
I just don't want the light touching the cfl lights despite what everyone says those fuckers DO get hot!
Absolutely.
CFLs definitely CAN burn plant tops if they get within 1-2 inches or so.
