I've done it a bunch of times and the difference is less than you would think.
It's natural to want to finish autos at 12/12 as that is where the non-autos
planted at the same time would be, just going from veg to flower mode.
First, do your vegging at 20/4 instead of 18/6. Most autos prefer a 20/4 cycle throughout
their lives. Most all non-autos will do the same/better vegging at 20/4 as 18/6.
Autos tend to be shorter, so when you flip from 20/4 to 12/12 you might want to do some redecorating.
Put the autos' pots on something that puts them closer to the light. The autos are giving up hours of light
and you want to help by giving them stronger light, eh? Also, I run autos in small pots so I water them
every day. Don't underwater autos if you can help it. They stunt easy if they get too dry young.
Good luck, BigSteve.