I haven't been able to replicate this. It looks like the tooltip still says 2 slots for vanilla beacons, but the actual beacon count reflects the changes made via Configurable Beacons. Is the tooltip what you were referring to?
I will need to reorganize how the extended descriptions get updated to fix the tooltip issue so that'll take longer to fix than usual. In the meantime, there's a startup setting for it as well if it becomes too much of an annoyance.