It was possible in the old Migaku Japanese Addon (https://ankiweb.net/shared/info/278530045).

But to simplify the process of setting up all the tools, all the old addons have been merged into on, the Migaku Anki Addon-on (https://ankiweb.net/shared/info/1846879528). Doing so we also removed some rarely used functions, as to simplify the UI and make it more user-friendly. So things like customizing pitch colors or converting 新字体 into 旧字体 have been removed.
Some functions are now also executed by the Browser Extension itself, as this is where they are definitely needed.

The old addon can still be used, but its only usable with Anki .35 and will not work on the newest version, which is required for the Browser Extension to work.

Currently its not planned to bring back this function as there dose not seem to be any real demand for it. If there is demand maybe, but not as it stands currently. So for now the colors used for pitch patterns (red, orange, blue, green, violet) are fixed.