The main (conceptual) problem is that instruments are not necessarily bound to tracks.
Perhaps the important word here is the small "necessarily"... because it's entirely possible to route the output of an instrument (both plugins and sample-based instruments) to a track. Even, multiple tracks.
These are the possible scenarios:
1. No track routing - can play on multiple tracks at the same time. Only possible with sample based instruments (.xrni) that doesn't have a DSP chain.
2. "Soft" routing, e.g. a plugin or .xrni with FX. Will output sound to whichever track the notes appear in.
3. "Hard" routing to single track. For example, a plugin with one or two channels of audio routed to a specific track, or a .xrni with a single, routed DSP chain.
4. Any combination of the above - e.g. mixed soft-routing and hard routing to one or more tracks. Possible with multi-out plugins, or .xrni with multiple DSP chains.
I'm not against using color. But to me, it's not desirable to have "instrument colors" on top of track colors.
Instead, I would like to see colors appear alongside instruments when/if some kind of routing is taking place.
For example, imagine you have a "soft-routed" instrument, used in multiple tracks? It could update (change color) in order to signal that it's notes are spread across multiple different tracks.
That alone would be very useful IMHO.