Rather than having a monolithic list of incompatibilities in the .tp2 file, I'm envisioning a few lines in each component, with the various REQUIRE_PREDICATE, FORBID_COMPONENT, SUBCOMPONENT, GROUP, and DESIGNATED flags (etc.) It will start out with only a few such notes in each component, or even none; and modders can easily add more as reports come in. And because it's just a two-way notification, unlike FORBID_COMPONENT which is a one-way forbiddance that relies on install order, active modders can note incompatibilities with inactive mods, and it work even though the inactive mod is never updated.
I know you've worked on BWS for a long time, and done good work there; but I'm not sure the BWS method that you inherited is the best. Relying on a single person to stay on top of compatibility issues is just too much work... and here, that person would be Wisp. Unless Zeitgeist allows for some kind of 3rd-party plugin... but even then, it would still be a single person tasked with handling it. Why not spread that burden to modders themselves?
Fact is, componenent numbers should not really change once a mod is released in "v1" status. And component numbers almost never change in old, inactive mods. So while it's a potential point of failure, it would be rare, and it would be very simple to address with an update.