You're right, the track shading is based on the min/max elevation of all tracks loaded. Simple solution - hit CTRL-A and then right click to disable them all. Then turn on only your temperature track.
I do plan to allow manual setting of the ranges for shading, but it's not there yet.
I'm not sure how you would shade waypoints, or what useful effect it might have. Shade the color of the font for the waypoint text being displayed, perhaps? I suppose it could be interesting with enough waypoints. Maybe you can describe more what you want to do with it.