Can config options be added to disable individual pieces of RFTools, not registering the items or mentioning them in the in-game manual? For example:

• A "teleportation" option that would disable the matter receiver and all other teleporting-related blocks and items
• An "endergenic" option that would disable the endergenic generator, pearl injector, and ender monitor
• Individual options to disable more-or-less standalone things like the coal generator and elevator

This could be achieved with MineTweaker, by just removing the recipes.

True, but then they'd still be referenced in the manual and would still exist in the Forge registries.