I've been following this for a while, but quite. In the annex, you say:
@principia_initial_state:FOR[AdditionalRealBodies]:NEEDS[RealSolarSystem]:FINAL

The presence of the :FOR[] and :FINAL conditionals will throw errors. The latest release of MM now reveals these, previously silent, errors. Only the first conditional (:FOR[]) will be processed while any others (:FINAL) after will cause the error and be ignored.

Additionally, your :AFTER[Principia], to be used by other modders, will be processed because of the existence of a Principia folder or DLL and won't be affected by the absence of :FOR[Principia].

Ah, right, FIRST, BEFORE[], FOR[], AFTER[], and FINAL are mutually exclusive; further, they qualify patches only.
Our principia_initial_state:NEEDS[RealSolarSystem] and principia_gravity_model:NEEDS[RealSolarSystem] nodes are not patches, merely nodes conditioned on a NEEDS[] clause, so if RealSolarSystem is present, they will be added as part of CheckNeeds, before any of the patch passes run; there is no need for patchers to specify ordering.

@7ranceaddic7, Note that FIRST, FOR[], and FINAL are not conditionals, merely ordering directives: a FOR will cause a (non-DLL) mod pass to be added by ModuleManager, and the patch will (unconditionally) run there.
Also note that the DLL called principia is not a managed DLL, and will not be seen by ModuleManager (ksp_plugin_adapter will, but we don't want people to depend on that name). The "mods by directory" feature will indeed find "Principia"; however since we have no patches there is no point for other modders in running in any of our passes. There could be some use for a :NEEDS[Principia] clause, if modders wish to make Principia-only adjustments to their mods.

I have updated the documentation to reflect all of the above; our configurations are fine as they are.