All of my tries at turning Rome into a 5-slot city eventually ended up in an autosave that always crashes when the turn is ended.

I think this may be causing this problem when the startpos.esf is changed. It's in campaign_map_settlements.xml (raw db files):

<campaign_map_settlements>
<settlement_id>settlement:the_papal_states:rome</settlement_id>
<region>the_papal_states</region>
<default_onscreen_name>Rome</default_onscreen_name>
<template_name>eur_4_slot</template_name>
<slot_count>4</slot_count>
<slot_type>settlement</slot_type>
[...]
</campaign_map_settlements>
As you can see by the lines in bold, the info here won't match the .esf, unstabilizing the game.
Please ignore if this is not important.