Yes, I can guess that. But the configuration is just illusional unless you select the proper “wiring layout”. Selecting the “Mcp23017 encoders” works, but “Custom” doesn’t work. Still, both “layouts” offer the same configuration options.
The “wiring layouts” and their cryptic names have allways been a mystery to me. Now I have traced them in the sources and it seems a lot of behaviour is just hardwired to their names, whatever the additional settings are. The “V5” seems to be an extreme: not only it does not offer any customization, but it goes as far as breaking the touchscreen calibration. I do not dare to file it as an issue (as @riban suggested), because it looks more like a feature than a bug.
But “layouts” that offer customization and yet have no effect at all (e.g “Custom”) seem far worse to me.