Hm, the 90001 values is from an EV_MSC input, which is a button or joystick input, I don't think it needs to be mapped.
According to this issue, the "EG Starts Arcade" kit should be supported automatically. There's even a .cfg file posted there.
Maybe the launcher is trying to configure your keyboard instead of the controller ? Have you tried starting a MakeArcade game with only the controller kit connected ?
If that doesn't work, you may try open an issue on @Vegz78's repo, I unfortunately have no experience with the MakeArcade setup - I just know they've been working to make this work as seamless as possible in RetroPie and other gaming oriented projects (Recalbox and Batocera).