Pretty sure this doesn't come from Kodi. It is likely coming from projector, AVR or splitter.
It depends exactly on how these are connected. Giving a list of hdmi cables connected from device A to device B may help me understand that.
Personally I'd start from the simplest setup (pi connected to projector) and check if that works (without the "Notice") and add the splitter then AVR back in one at a time and see at which point it appears.
Sorry about the false alarm regarding me believing the notice was something coming from Kodi.
You are correct popcornmix, the notice was coming from my AVR for some reason (it's a 4K AVR with all the correct cables). I didn't spot it at first since I have all of my remotes (TV, projector, AVR, RPi5 etc) mapped to a Harmony 525 (an oldie but goodie) and had misplaced the AVR remote - when I found it and pressed the Ok button the notice disappeared and I can watch in 3D.
A problem for me to solve is why a relatively new 4K AVR (with HDMI 2.0 cables) doesn't correctly recognise a 3D signal to pass through from the Pi (fyi: it's Pi to AVR to powered splitter to 2D TV + 3D projector) but I'll try doing as you suggest in your last paragraph.