lldc13 to your question 1 my answer is yes the penalty would be recalculated. My understanding is that this already happens with TRS itself as it's a net sum zero stat and updates as league averages fluctuate through the year.
What I propose is just for the penalty. The base TRS for the player is their MLB TRS. They need to play in MLB and be active on a Mendoza roster the same day to collect the IP and TRS.
As far as difficulty to code, I'd look to Arne for guidance, but I'm pretty confident I could code this reliably.
Robinson - Jobu's Lumber and Gas Mendoza - Slicing Fair