Thanks for your feedback Metin!
The message you see is a warning I’ve put to make sure that anyone who wants to use my material operators switch to Cycles. And atm, this message indeed stays active, even if you are in Cycles. At least you understood you had to go to Cycles
THE OPTION TO BAKE TEXTURES TO TEXTURES WORKS WITH SELECTED TO ACTIVE AT THE MOMENT. SO FIRST SELECT YOUR HIGHRES MATERIAL, THEN YOUR LOWPOLY ONE. It should get activated and you should be able to do the baking.
AGAIN: I am getting overwhelmed and answering in a rush, wait a few days, and I hope I’ll have everything nicely setup in a more comprehensive way.
The baking to vertex colros only indeed bakes the albedo channel, so that’s the expected (just not well explained) behaviour.
The UI for the materials is not clear at all, and It will probably be in one of the next few releases.
Finally: thank you so much for your motivation, that’s the kind of feedback that will keep me trying to turn BakeMyScan into somewhat of your “ultimate” addon. For free ! And also, sorry if the answer is confusing, I don’t have the force to read myself back at this point