I ran into this same problem.
I'm using an MPK 88.
I created 16 External MIDI Instrument Tracks.
What I found out I had to do was select "index" and put a number with that - so that 2 controlled track 2 whether it's selected or not. The MPK88 has three control banks for the faders/knobs/buttons. So I set up the 8 faders to control tracks 1-8 and then "Control Bank B" to control tracks 9-16.
Click "learn", then move the slider on the track you want to affect, then move the fader on the keyboard. Then go to Expert View if not already there and it looks like this:
So notice Volume 1 is selected in the 2nd pane, and then I have "index" selected with a 1 after it.
If I were to click Volume 2 (or move the fader that's assigned to it, which will automatically select it) it looks the same except the index says "2" after it (of course the message numbers are different).
(the exclusive box - I don't know what it does but I was trying everything to get this to work so it's checked on this one but I don't think it is on the others).
By setting up 16 like this, the 16 MIDI tracks I had could be controlled with the keyboard faders 1-8, and then I could switch to control bank B and have those same 8 keyboard faders controll 9-16.
I came in this morning and it's all still set up and working, so looks good.
I just tried this - I deleted all the tracks from my 16 track MIDI template and added a track of each type and they all still worked - Fader 1 controlled Track 1 (software instrument) fader 2 controlled track 2 (audio instrument) and so on. If you delete a track - like Track 3, and Track 4 moves up into its place and becomes Track 3, Fader 3 affects it. So it's based on position this way.
HTH a little.