This is exactly like the mupen64plus-gles2n64 line EXCEPT, I modified the text before the = sign (adding mkcheat) and added the command-line option for the cheat at the end, though before the %ROM% variable. The 0 represents the number of the cheat code (Infinite Items) and the 3 represents the option (Invincibility Star) which gives us –cheats 0-3.
Now, what this does is give you an additional “emulator” to choose from when you configure the game/emu by hitting X or M after launching from EmulationStation. Change the default emulator+rom option to the “mkcheat” version and mupen should attempt to launch with cheats enabled.
I spoke too soon, it seems some of the codes work without producing the segmentation fault error. Digging deep into Google search results came up with at least one other person experiencing the issue under Ubuntu but there did not seem to be an actual resolution.
Marking this as resolved as it does not appear to be specific to RetroPie.
Hopefully someone will at least the cheat workaround I posted above helpful.