As the clearances have gotten narrower and narrower the fudge window (of how all meshes with each other) has also gotten less. Not mentioned was when the wheel (with it's own cassette) or the original cassette were changed is if the read der cable "index" tension was also reset. If not then the very slight difference of cog location WRT the der's indexing position might not have been well coordinated.

As to the chain plate's differing scalloping I strongly doubt they are a factor for your issue. The plate's contours are more about the shifting smoothness and responsiveness then effecting after shift chain rub.

other things to check out are the cable condition, the guide pulley's wear and that cure all (by many people's claim) a bent der hanger. Andy