Hmm well the thing is in EU4, the forced PU modifier wears off quickly so they never rebel or try to break off.
Maybe forced PUs need a hefty liberty desire penalty that slowly decays...
It should pretty much never wear off, the Portuguese got free after 60 years a very long time period: "This situation culminated in a revolution organized by the nobility and
bourgeoisie, executed on 1 December 1640, sixty years after the crowning of
Philip I (Philip II of Spain), the first "dual monarch"."
Integration should probably lead to war always?
As for religion, how did that cause the PU to break? The senior partner tried to convert the junior partner and they rebelled?
Just good old fashioned and brutal religious persecution:
en.wikipedia.org
"Section III, expanding on the existing legislation, enacted that if a Catholic priest took Mass, etc., as above; or if any Catholic clergy or layperson ran a school or "take upon themselves the Education or Government or Boarding of Youth"; then they were, on conviction, liable to "perpetuall Imprisonment" at the discretion of the King. Despite its severity, Section III was to some extent a mitigation of the provisions of the
Jesuits, etc. Act 1584, which prescribed the death penalty for any priest who failed to leave England within 40 days of being so ordered."
I don't know what the situation was in the Netherlands, but I wouldn't be surprised if it was a mirror image of the above (so catholics opressing protestants instead of the inverse in the UK).