Apriltools now tracks all tags in the frame instead of only the first one.
Instead of selecting "moving camera, fixed tag" or "moving tag, fixed camera," you can choose a single "static tag" to base the camera movement off of and the other tags will move relative to that fixed tag.
There still isn't any way to use multiple fixed tags to track the camera or many tags on a single object because there isn't a clear good way to combine multiple tracks together into one, but I'm sure you could at least use blender to average together the position of multiple tags.
Apriltools now tracks all tags in the frame instead of only the first one. Instead of selecting "moving camera, fixed tag" or "moving tag, fixed camera," you can choose a single "static tag" to base the camera movement off of and the other tags will move relative to that fixed tag. There still isn't any way to use multiple fixed tags to track the camera or many tags on a single object because there isn't a clear good way to combine multiple tracks together into one, but I'm sure you could at least use blender to average together the position of multiple tags.