It seems that you have good ideas here but I must raise some issues:
1. This could be micro-intensive in a bad way: because of the current limit of 5 Magistrates, the player will no longer have to build 200 workshops at a time, but instead, he'll have to build 5 workshops every 5 months (example, of course, subject to income of magistrates, but still). (
This is not theoretical: I already have this problem in HTTT with roads)
2. If there is no system to automatically spend extra magistrates, this may bring us back to the old reality where you have to click every province one by one to make your upgrades.
(Remember the sweet joy of trying to find WHICH "More Than Three Provinces needs a Temple", knowing you'd only know once you wittled it down to Three?)
We have to keep in mind most EU3 players manage Large Empires.
My suggestions: Increase the limit of maximum magistrates and export this value to Defines.
AND/OR
Make it so that any magistrate income past 5.00 is automatically spent on building non-unique structures in the provinces where the AI thinks it makes the most sense.
Without either of this, the game could increase in frustration for large empire instead of becoming most fun. Even now in HTTT, we have this problem to an extent with decisions. Please dont overlook