Giving promotions to missionaries brings us back to the original problem with 3 spreads: you only need 1 church on empire, and then you can funnel all missionary purchases through 1 city.
Boosting missionaries is best done with wonders or beliefs, things with global effects. The church's bonuses should be constrained to the city they are built in.
Churches often sponsor missionaries IRL. Maybe a small gold bonus in city with a church with every missionary action? Then move the conversion strength bonus to Borobudur as previously discussed.
Church:
+4
Faith
20% resistance to conversion in city
+50% religious pressure emanating from city
On missionary spread, 10
Gold in city, Scaling with Era
Reduces Poverty
Exact gold amount is up for debate, not sure what would be balanced. I think poverty reduction, same as cathedral, is more appropriate than boredom.
Borobudur:
+5
Faith
Free Stupa in City
Free Missionary in City
Missionaries have +25% Conversion Strength
Missionaries ignore terrain costs when moving
Either ignore terrain or can use enemy roads. Whichever is preferred