All the CORE OPTIONS are stored there. That doesn’t change anything. The multitap configuration is not standard, as in core devs implement that differently. Ekeeke implemented it using controllers in mednafen. In mednafen it’s just a toggle that enables additional ports.
This can be “per-core” if you use a different config yes. But since sometimes it will be a different “controller” as in genplusgx and sometimes it’s a core option that toggles the option it’s not exposed as you would expect.
I was asked to expose it as a controller option when I implemented it in yabause as documented in https://github.com/libretro/yabause/pull/7 so I’m guessing that controller is now the preferred way although personally I think it clutters up the controllers interface.
Out of interest, what did you do to get J-Cart working?
I’m using RetroArch with the Genesis Plus GX emulator chosen. I see that RetroArch recognises 4 controllers, but in game they are not detected.
(All packages up to date as of today.)