Regarding the CB changes: the way it works now is that you can still take provinces as long you also take your primary war goal.
For example: a very popular strategy is to take the Cheb gold mine as Austria in the PU war. The way it works now is that you cannot select any provinces until you have the "Union with Bohemia" peace treaty selected. If you have done then you can conquer provinces atop of it.
In a way, it works like the Independence War works in 1.32 - you cannot take provinces unless you also demand your independence.
The parliament changes are mostly for modders than for the game itself. Before the change, the nobles estate would always vanish if you have the parliament trait active. With this change, however, it is now possible that you can mod a parliament mechanic to a government without forcing the nobles out of your country.
The functionality of the 5th reform has not been changed though. If you enact you still remove the nobility estate from your country and gain all their crownland as intended.
Regarding the dip rep stacking: I
think this is a byproduct of a change which allows the stacking of country modifiers. However, I do not have a definitive answer if that is intended or not though.
Fortunately, there is an estate privilege which allows you to annex vassals without getting a dip rep hit though