You can already do this! If you just don't delete the old folder "Pandemonium Classic - Unity Edition" and extract the new version you downloaded over it, then it'll update all the files (it'll want to replace 190 or so) and let you keep your spawn tables, rule settings and everything else. I've been doing that for years and it's only caused a conflict once, so you can safely do it that way
There's also a file called "settings.txt" (Pandemonium Classic - Unity Edition\Pandemonium Classic - Unity Edition_Data\settings.txt), which is the file that contains all these things. You can pass that file around or copy-paste it into new versions to keep all your settings.
Well dang, that would have saved me a lot of time, lol.
So I finally got around to trying the new content. The new custom sides mechanic is neat, though I've already found two... I don't know if I'd call them "bugs", but stuff that probably shouldn't happen. One is that allied Rusalka still only target humans with their secondary power. However, once a human is under their power and starts following them around, they can't transform that human, and they never recover from that state, so they're pretty much stuck that way. Allied cheerleaders are also an issue since the dark ones still cheer for monsters, but you can't attack them to bring them back to your side.
Then there's... This.
I'm not sure what that slanted thing is supposed to be, but it's probably not supposed to block that door or overlap that table, and almost definitely not supposed to trap poor Sanya inside of it when she spawns there.
Anywho, are there any future plans on expanding the faction mechanic? Like, for instance, allowing some monsters and items to change a target's faction without transforming them (possibly including reworking the mechanics of some existing ones like the Hypnogun)? Maybe with a separate "monster type" in the group affiliations tab dedicated to the target of that attack/item, like for instance having "monsters hit with Hypnogun" that can be assigned to the Human faction or something like that.
With that in mind, while monsters transforming monsters may not be an option (with specific exceptions like the fallen cupid), maybe some of them could still convert other monsters to their faction (or another)? Perhaps it could be an automatic behavior you can set in the faction menu, e.g. one faction targets another as "Convert" instead of "Hostile", which is functionally the same but causes them to switch sides instead of dying when killed. And/or it can be tied to specific monsters as their unique ability, like a mind-controlling parasite that all monsters see as a threat because of its ability to turn any of them into its puppets.
But the monster concept I think would be the most fitting for a mechanic like that would be the Monster Tamer, or Beastmaster, or something like that. It would be a "human-type" monster like the Maid or Hypnotist, driven mad by her desire to dominate all monsters and make them her slaves, and she would have her own faction and be hostile to everything (by default). Monsters she defeats would join her faction, and humans she defeats would be collared and "tamed", turning into her loyal pets. Maybe after meeting certain conditions (like getting enough headpats), the human pets can be promoted into another, fully inhuman monster type exclusive to the Beastmaster's slaves. (But not into a fellow Beastmaster - there can be only one true mistress!)
Last and probably also least, if the ability to change someone's faction mid-game is added, maybe it could also be possible to let the player choose a separate faction to start as, separate from their chosen race? Then maybe I could finally make my fantasy game mode where you play as a human enslaving the other humans while trying not to get turned into a monster.