I think that the way tracks can be managed in PD is already fairly good.
When adding a FX-track (which btw is a bit cumbersome, why not make that a bit easier CL, like a menu option to add one FX-track?) instead of making the number of audio tracks 0, because of a typo I added 10 audio tracks (10 instead of 0). Then I removed the empty tracks, which resulted in 3 audio tracks only. Maybe it is a feature. When playing a bit more with the adding and removing of tracks, it looked (as far as I could see) a bit inconsistent. One can remove empty tracks, but the first 3 remain. And the remove track option is disabled for the first 3 tracks. In some cases, one ends up with an audio only track as track number 1, which can only be deleted, when moved to the 4th place.
(I have submitted this as a suggestion to CL.)