Ok I hear you and I think you are right. It's not obvious enough at all how the stats work.
If you want to keep trying, the way to benefit from the skill trainer is to uncover one of the nearby blue rocks (the one below him is easiest) and you can get a resource to bring him from there, that will teach you a skill that will give you a bigger immediate benefit.
As for the stats, the permanent one is just an XP multiplier for the stat. The daily level is the only one that impacts your power level (until you get the STAT skill). So, the permanent level makes a bigger difference in longer loops which give the stat more time to build up.
I'm not telling you to accept any of that as a solution, I would definitely do some things differently now.