Did some more testing, and determined that the "Lost colony" origin issue wasn't related to the mod. I'm still not sure how that extra empire spawned; during testing the "Lost Colony" origin I had a similar situation where two advanced empires spawned for one Lost Colony empire.

A couple of other notes. I noticed quite a few random Gaia world floating around, which I assume is a feature of this mod. If so, props to you, because it's a nice touch. I did find one being orbitted by a larger planet though...perhaps that has more to do with 5x planets. Also, one of my custom empires that had the "Lost Colony" origin instead spawned with the "Prosperous Unification" origin (everything else about the empire seemed normal). I confirmed that the origin hadn't been changed on the new game screen after I quit the test. I am wondering if the unexplained 41st ai empire was supposed to be this empire's "home" empire but instead generated as a random? I'm assuming this is related to YAGEM somehow.

Apologies if these issues are already known, and sorry about the text wall; this is my first dip into running Stellaris modded. Not sure if anything here could be lurking and causing issues in the live version of YAGEM; I haven't played any versions of the game past 3.14.

...First primitive reached ftl four years into the test, and the game was fine. I let it run until 2220, during which time four more primitives reached ftl, making 46 ai empires and 55 "empires" total, plus dozens of preftls. During this time the game ran great, generally only lagging when it autosaved or I zoomed into a system. Considering this, I have no idea why trying to set more than 37 ai at the start crashes the game. It certainly handles them in game fine, and there is certainly space in the 3k galaxy for more (it could easily fit 70 and everyone would still have room to expand, with max FEs and marauders).

I decided to run a test on the Colossal (3000 stars) galaxy size: 36 ai empires (no advanced starts), 5 fallen empires, 3 marauder clans, and the caravaneers. 5x hab worlds and presapients/preftls, 1x hyperlanes, no L Cluster or abandoned Gateways. Took a few minutes to generate, but the map loaded fine. Set human_ai and observe commands to look around; all 36 ai empires spawned (33 being customs, not sure if that matters), as well as all 5 fallen empires,all 3 marauder clans, and Chor's Compass. As an added bonus, the Chosen existed (almost touching another star cluster, which was pretty funny), one of the ai had a federation origin, another ai had a human origin spawning the CoM, and there was an extra ai empire spawned that I couldn't determine the origin of, bringing the total number of "empires" (if I'm not misusing the term here) to 50 at the start (41 ai, 5 fallen, 3 marauder, and caravaneers)...

Running this mod with your 3.14 (Circinus) Unofficial Patch (UP loaded first, this second, no other mods); the galaxy sizes "Nano", "Colossal 4k", "Colossal 5k", and "Colossal 6k" can not be scrolled to on the new game page without immediately crashing the game. This isn't a big deal, since gigantic maps inevitably get lag issues (losing Nano's a bit of a bummer though). Additionally, attempting to set the ai count to above 37 immediately crashes the game as well. I suspect this is why the largest 3 map settings crash the game - based on the default ai counts for the other map sizes "Colossal 4k" and above have a default ai count above 37, causing a crash. This does not explain Nano crashing though, and I don't have any theories why it is doing so (Unless it is trying to load a negative amount of ai? Is that even possible?).