There is a general message that "Some of the achievements will be disabled with the current settings because: ... Proceed"
The list of disabled achievements, and reasons, is empty, and all achievements show as available in the game's achievement listing.
You may, or may not, be able to suppress the alert, but it's probably not worth it. For one, it's showing that the list is now empty - the mod is working, and second, if you're using the mod, you probably already know what you're doing.
It might, however, be worth a note on the information page that it pops up. I've not tested it, but it likely is the same for the non-SA variant.
