I installed the conversion kit into my RV-10 wing tips and mounted the landing lights and nav/strobe lights prior to fitting the tips to the wings. While I'm not flying yet, as far as I can tell it worked well, and it certainly didn't seem to impact my installation of the tips to the wings.
I also believe it made the cutting and fiber glassing in of the conversion tips much easier as I was able to work on the bench with full access to the inside and outside of the tips.
I can't say the same will be true for the RV-9, but I suspect the same would be true.