You got that right, with the only exception that you will need to copy any files you want to modify from \Default to \ProfitUI, because the patcher will replace any modifications made to \Default.
Loot auto accept all is not in ProfitUI (there are mods though), but it should be accepting on hitting Enter unless I forgot to readd that. I'll check, I think I forgot to add it to the Greed option anyway.