Just FYI I did look at the code... it does have all the adjustments that I mentioned (player comps, position adjustments, skill adjustments, trait adjustments, playing time, bumps for highly prized attributes, etc.)
So yea, it's pretty much working as intended. Again, if you find specific examples that I can test for or add scenario checks I'm open to ideas. So far I'm not seeing anything systemically broken (or it's something specific to your league setup and not something I can code for without breaking everyone else playing the game). We can revisit in the next version if we want to change up the way all of this works, or if we want to add additional checks or options for leagues to choose their own path.