Maybe I'm just slow or not used to using workarounds, so I couldn't figure it out at first. Perhaps it's more picky if you bought through steam and needs to be run through steam to detect the dlc you've bought? No idea, and I'm letting myself be distracted.
To elaborate on his solution, to work with steam, switch the names of the x86 and x64 around. Then run from Steam. The trainer will find the game and run as per usual. Or at least, the skills and ability points works.