Hey wanted to report a bug and I don't think I saw anything exactly the same.
I was using the most recent version of the mod (installed ~1 week ago) along with improved water yields, cqui, unit report screen, and AI+ with the winter patch installed.
I was playing on a large island plates map with 10 players (standard) with the turn limit turned off in advanced options as Victoria and restarted several times until I got a starting island I liked. Played through the entire game to a culture victory (before the turn limit so I don't know if that stayed), realizing once I started large scale exploration the map seemed rather empty. Assuming a few civs got rushed I didn't think too much of it and just colonized where I wanted. The score screen at the end confirmed 3 civs were "supposed" to be in the game but never spawned. They were listed on the score screen but had no units lost, no cities lost, no stats whatsoever. I'm assuming this is a bug with restart button, or maybe even Civ 6 in general. I don't think the other mods I have active would do anything like not spawn a civ, maybe AI+ would send initial settlers to get captured but I would think that would show as a unit lost still.
Going to reinstall again just in case, will report back if i see this again. I'm a compulsive restarter so this mod makes my games way easier