The regionfree hack deals with game_region setting (0x14C in seeprom) and is unrelated to gamepad woes.
There is a separate setting product_area at 0x148 which is much more important for the current topic.
When you run SysConfigTool, you can see these separate settings, as well as the language settings:
If we would try to fix this from the WiiU side, we would need to change the 'Platform Region' setting there. It might also be necessary to change the 'Country' setting.
I would prefer for the solution to be on the gamepad side because it's less intrusive, less likely to brick your system, and in case something goes wrong it's cheaper to replace gamepad motherboard than the Wii U.
For those that would still like to try the WiiU side, please keep in mind that you shouln't install the normal, system version of the SysConfigTool to sysnand, because it's a system title and it will overwrite your home menu and settings.
Use the repackaged .app version instead.