Sorry for the late response, and I agree that the reversed button layout wouldn't make playing this very fun.

What operating system are you using to play the game? As each line in gamecontrollerdb.txt only works for either Windows/macOS/Linux due to the code you see at the beginning. The Wii U Pro pad seems to appear in the Windows list, and shows the following:

> 030000007e0500003003000000000000,Wii U Pro,a:b0,b:b1,back:b8,dpdown:b14,dpleft:b15,dpright:b16,dpup:b13,leftshoulder:b6,leftstick:b11,lefttrigger:b4, leftx:a0,lefty:a1,rightshoulder:b7,rightstick:b12,righttrigger:b5,rightx:a2,righty:a3,start:b9,x:b3,y:b2,platf orm:Windows,

If you want to swap those Y/X -> X/Y and B/A -> A/B front buttons I would completely replace the whole file (just to make sure) with something like this, you can see I changed b0 to b1, b1 to b0, b2 to b3 and b3 to b2:

> 030000007e0500003003000000000000,Wii U Pro,a:b1,b:b0,back:b8,dpdown:b14,dpleft:b15,dpright:b16,dpup:b13,leftshoulder:b6,leftstick:b11,lefttrigger:b4, leftx:a0,lefty:a1,rightshoulder:b7,rightstick:b12,righttrigger:b5,rightx:a2,righty:a3,start:b9,x:b2,y:b3,platf orm:Windows,

There is some visual SDL2 gamepad mapping software compatible with this format for all three supported operating systems that should make your life easier, Steam also supports it out of the box. The standalone game may eventually gain this capability to make it simpler.

Here is one I've used before: https://generalarcade.com/gamepadtool/

Hope that helps.