hello jason, you could try to delete the file named pluginreg.dat in the affected profiles, then all the present plugins will be set to active again...

I would need it to apply to the machine and not just users, just like locked preferences overrides the user profiles.

It would also be nice if I could enable specific plugins since there are other disabled plugins that would best remain disabled.

as far as i know this can't be done in about:config unfortunately, since the pluginreg.dat file is the only place where the information about the status of plugins is stored. one thing you could try on a machine level is to move the location of the plugin's .dll file (maybe to the \plugins subfolder inside the firefox installation directory), then it may be re-detected and treated as new plugin which should be set to active...

I figured out you can refer to specific add-ons in preferences using extensions.<GUID>.property, but I couldn't find any documentation and it appears to only work on themes and extensions and not plugins.