Taxes will change slightly as part of the new estate changes. However, they will still be derived directly from the region and paid to the knight. There will be no return to the "realm collects it all, the parcels it back out to the nobles" style system.
But you said yourself that "The new tax system is great at handling steady-state stuff. If your realm neither gains nor loses regions, it works just fine. But it simply cannot adapt fast enough to handle acquiring and losing regions".
Will the new estates be able to adapt fast enough to handle acquiring and losing regions? If not, we're stuck with the slow pace aren't we?