I don't think mixing-up Papal states, regalian bishopries and monastic states as a same ensemble of clerical states is quite accurate, even less to consider them as theocratic monarchies.
Among other exemples :
- Rome didn't as much was suzerain of Rimini because "God told so", but because they were the secular rulers of the region.
- Prince-bishopries in HRE, even after the Investiture Quarrel, remained largely tied to their relationship with the emperors and owed their legitimacy from it, not "God gave me this". Eventually, as it happened in many urban bishopries (not just in HRE, but as well in southern France and Italy), while you had a clerical head of state didn't meant that local elites didn't deeply played a political role
- Monastic states were really, really, tied to the nobiliar situation : while some were technically dependent from HRE, Jerusalem or Papal states, they were often the bed of Latin, often French or German, nobility to the point some of their institutions were indirectly inherited by states (St John Order as a predecessor to Ecole Navale, for exemple).
That being said, the existence of clerical fiefs is due to the existence of feudal polities in first place : you can't have these if you get rid of the latter.
You could argue that they could somehow become "clerical" kingdoms, but I doubt it : the only real tentative was made by Alfonso I of Aragon
that wanted to give his realm to fighting orders. It was laughed off (mostly because kings can't dispose freely of their kingdoms, especially the parts they inherited), and everyone resumed to find a successor.
At best you could see the development of princeley bishopries in regions as southern France (out of Provencal "patricedoms", for exemple), but it wouldn't be that obvious. The best way would be, IMO, to carry on with the IOTL development more than IOTL, as in feudalized or feudal clerical polities.