I've been using a Thule Motion XT box with my Toyota OEM cross bars for 4 years now (2019 4Runner ). it does sit very close to the rear 'shark fin' fairing but no issues at all
just got the infinity's in my 4Runner....sounds amazing. has anyone who's done this had issues with the drivers side tweeter fitting? there's some ductwork on that side that interferes. I got it stuffed in there but just barely