Many of the rules are written to be a bit on the vague side so the "rules" don't box you in to something that doesn't work with your story. If you come across some gray areas then just do what fits best.
For any roll that creates a new faction I would consider them a completely new entity, however, there's a few instances where you could consider them merged. The hive creating a monster is one of those instances, it could be a new queen that still lives with the hive, or, you could treat it as an ally that still rolls separately between ages but treats the hive as an ally and works together. Basically, it's up to whoever rolls to create the story and meaning of that result.
There are a few things that are meant to be map "beautifiers" and the shrine would be one of them. Little things like monuments, shrines, & landmarks to help add some fantasy character to the map.
You can also use shrines as an excuse to get your gods more involved in the story. The Pantheon section doesn't really do anything for the game unless you choose to use them. They are there to help you get ideas and create stories for certain groups. (New cult pops up and have a god of the moon. Maybe they're werebeasts?)
Heroes is something I've been thinking about for a long time but I haven't figured the best way to implement them. Either way, they'll be more for story than actually doing much to sway a roll or faction.
Thanks for the questions, I hope I've been somewhat helpful.
-Nook