I'm an owner at Codetree - one of the project management launch partners for Marketplace. We talked through this scenario with GH when we were integrating.
What happens today is the limits are enforced on the app side, not he GitHub side.
So for example our free plan is two users. If you wanted to add a third you'd need to go GH Marketplace and upgrade to the eg 10 user plan. That would trigger an upgrade in Codetree and your plan there would enable you to add up to ten users.
In short: you trigger upgrades and downgrades, not the tool vendor you're using or GH, and thresholds are stored in the tool vendors database so they're the ones who decide how to tell you that you need to upgrade.
What happens today is the limits are enforced on the app side, not he GitHub side.
So for example our free plan is two users. If you wanted to add a third you'd need to go GH Marketplace and upgrade to the eg 10 user plan. That would trigger an upgrade in Codetree and your plan there would enable you to add up to ten users.
In short: you trigger upgrades and downgrades, not the tool vendor you're using or GH, and thresholds are stored in the tool vendors database so they're the ones who decide how to tell you that you need to upgrade.