Hi there!
I never used Capacitor and even don't know what is this. So I can't speak for sure that has something to do with it. This is a hard thing to debug. On my attempts using Android studio it works fine. When you mean does not work, an error happen? Or the controls just are not showing up?
I can think of two things for you to try:
1 - Set the parameter "Fix Button Size" to true.
2 - Android has a behavior that is not the same as the windows about filenames. Meaning on windows the filename "dpad.png" is the same as "Dpad.png". But, not in android. So, maybe you can try double check the filenames in the folder and the ones that are on the plugin parameters, to see if they are exactly the same, including the lower/upper cases.
3 - If you are excluding uned files on deploy, make sure the files for the mobile controls are there on the deployed project before you export for android.
Besides that, I don't know what can be wrong.