I want players to bring their own parts.  Is this in the config somewhere that I am missing?

Don't grant any of the spawnmodularcar.engineparts.* permissions. After that, if you still see parts when spawning cars via this plugin, the parts are added by other plugins.

It was the TalkingNpc plugin that spawns the cars that sets engine parts, sorry for the mistake.  Hopefully that helps anyone else if they run into this and miss it in the config.  Thank you.