there would be no trainer at all if I had not taken it over
Do you own the game on Steam or GOG? - The trainer is written for the STEAM version.
I am having the same issue. Setting the skill level will not unlock any of the related perks, in my experience.
A possible solution would be to replace the "set skill" option with an "add XP for skill" option. That way you can level up normally while you sleep, and get all the recipes. As it is right now, you don't get any of the recipes when you set your skill level.
Other than that, all other options work great. Another great job!