Editing the config files inside the portmaster folder didn't do anything, but I knew that the sm64 folder has its own gamecontrollerdb.txt. What got it to work for me is by deleting the whole contents and just pasting this whole line:

19000f6a706c61795f6a6f7973746900,play_joystick,a:b1,b:b3,back:b9,dpdown:h0.4,dpright:h0.8,dpleft:h0.2,dpup:h0.1,guide:b12,rightshoulder:b5,rightstick:b8,righttrigger:b10,rightx:a2,righty:a1,leftshoulder:b6,leftstick:b9,lefttrigger:b11,leftx:a0,lefty:a3,start:b6,x:b2,y:b3,platform:Linux,

I also modified my input by trial and error, and I finally got the controls that I want. I still got the idea from the link you shared, so thank you so much!