The waypoints are associated with the track they are assigned to, but you can find them in your saved waypoints folder, but you cannot toggle on/off your waypoints the way you can toggle on/off your tracks. Yes, you could upload a .gpx file that only has the waypoints and then you would be able to toggle them on/off as a track, just without the lines of a track. I did that this morning with a users .gpx file of waypoints for the Lycian Way in Turkey and that worked perfectly. Use that work around for now, but please put your idea on
UserVoice as well for a toggle on/off switch for waypoint or for a setting to turn off the track and just show the waypoints of a .gpx file.
I am glad you are enjoying Gaia GPS, and our customer support. We really value the input of so-called "power users" like yourself, you guys really get to know the app and tend to come up with great ideas for its improvements.