This is happening because AJE Extended depends on AJE which depends on FAR, and FAR isn't available for 1.4.2 (the forum thread title says specifically 1.3.1). So at one level this is a duplicate of #2231, since AJE Extended should be marked as incompatible (note that AJE itself is marked incompatible because of the incompatible dependency, but that doesn't propagate through multiple levels of dependencies).

At another level, it would be nice to automatically uncheck AJE Extended after the error is dismissed. Not sure how feasible that would be.

Yes, the first level doesn't matter to me, as I just wanted to install it for testing pusposes for #2416 :D
I think your second approach is the way to go, as just suppressing the error is both more complicated (I think, didn't check the code yet) and also not recommended, because suppressing errors always is a welcome opportunity for more errors to sneak in.

This should be easy, but WinForms continues to embody the principle of maximum surprise by not changing the checkbox's display until after I click somewhere else in the grid. The (new) code to uncheck the box runs, the mod is removed from the changeset, but the UI is sitting there with a check mark in the box. It's a wonder to me that people have been able to get anything done with this toolkit at all.