The Papacy is a unique case. It will never drift into an empire—either that, or it will always reset upon save load, I forget which. Anyway, it’s intended behavior that it shouldn’t have a de jure liege. As for the bug mentioned in your links, that’s a different thing.
Are you sure that you aren't mixing up two separate behaviors?
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k_jerusalem has the line
assimilate = no in the
landed_titles files. This means that duchies will never assimilate into or out of it, and that it will never assimilate into or out of empires (I think). Assimilation never progresses at all in-game.
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k_papacy isn't under a
de jure empire in the
landed_titles files. This means that, for
k_papacy (and for any custom kingdom), assimilation into an empire will
progress normally in-game (and the progress will be recorded properly in the savefile), but the
completed assimilation will
not be saved properly due to the vanilla bug, resulting in an instant de-assimilation when the savegame is loaded.
If the Papacy's failure to assimilate into empires is an intended feature in SWMH, maybe you should add
assimilate = no to
k_papacy in the
landed_titles files. This also would prevent it from assimilating Latium and becoming non-titular, however.