A fix has finally been found for the Pro Controller color issue!
First, set your colors like you normally would.
Then, open "More..." and go to "Debug" to open "Debug: Custom Command".
Set the following:
Cmd: 01
Subcmd: 11
Then click on "HD Rumble Player". This is necessary to trick the program into allowing you to set the Subcmd to 11, as it's normally disabled. Open "Debug: Custom Command" again
Subcmd arguments: 1B6000000102
Hit "Send" .You should get a Subcmd Reply starting with 80 11. You should be good to go then
I can confirm this worked! Thanks so much for sharing! That has been bugging me for a long time.