Actually... I've just made a proof of concept that detects Sancho Mod correctly.

I won't discuss technical details — not to give DPC bad ideas

— but it's feasible. He just didn't bother to.
(Or maybe he just dislikes Scrappy and tolerates Sancho... who knows?)
Sancho provided a "save fixer". It's just a small
.rpyc file that you can drop in your
game folder once you’ve uninstalled Sancho Mod (or if you're playing a new release for which a new version of Sancho mod is not available).
I successfully played Episode 11 (for which, AFAIK, the Sancho Mod is not available) starting from a save made with a Sancho-modded Episode 10 game, just using Sancho's save fixer.