Zotero is really giving me headaches with all these malfunctioning mime-types.

This is not a problem of Zotero's making. You're using an OS with about a half dozen different ways to configure file-opening behavior and no native file reveal functionality. All Zotero does is send things into that mess—it's up to you to make the system do what you want.

Out of curiosity, does Firefox's download list get this right, if you right-click and choose Open Containing Folder?

Specifically with file revealing, Zotero first tries to run Mozilla's file.reveal() function, and when that fails (which it generally does on Linux), it "launches" the parent folder via the OS, using Mozilla's file.launch() function. (What launching "via the OS" means on Linux is generally a deep mystery.) If that also fails—which can happen for various reasons, so you'd have to check for "launch() not supported -- trying fallback executable" in the debug output for the action to see whether that was the case—it runs the executable specified in extensions.zotero.fallbackLauncher.unix in about:config, which defaults to xdg-open. (I don't remember off-hand where xdg-open gets its settings, so if the debug output does indicate that that's being used, you could look into that.) And finally, if xdg-open also fails, it passes the file URL to Mozilla's external helper app (i.e., open/save) window.