You guys crack me up lol.
My car has been in for loads of warranty work (and just received my letter for the blower, didn't get one for the battery cable as that's not an issue on my car apparently
) and it being modified has never been an issue.
For something like the blower there is no need to flash the ECU etc or do anything recoding or updates unless they tell you as the idea is to just get your car in and out for this particular fix and move onto the next.
They will only do the recall unless otherwise specified (well that has been the case with me and different dealers over the last 15 years), so you should be ok.