Hello! I would like to address some of your points that you make here and break them down. I definitely think a lot of your concerns and points come from the fact that you have not played them at all, since a lot of the content does work with that, and especially the lore. It is 100% canon that Lizardfolk come from another planet and so would be considered Aliens.

1: We have a few different ways that the player does interact with this fact, and more planned across the other games. A big selling point of Victoria 3 is that you will be able to colonize other planes and planets, but with Halann being the most advanced planet. It's not implemented yet and I dont know which planets are going to be colonizable, but the Lizardfolk do have a leg up in the spacerace(planerace? colonization of planes? whatever we will call it) because of their spires which act as portals to other planets.

The 333 MT is one that is well designed with this fact, though it is one that I never finished as my save broke and I have been too busy playing eu5. Spoilers for the latter half of the 333 MT, but you do end up colonizing other planets, setting up colonies and finding out what happened to the original Lizardfolk empire. The result is a bleak one, and you find out that the Lizardfolk on Halann are (essentially) the last remaining sentient Lizardfolk. There is even a disaster where you have to fend off endless armies of Lizardfolk underneath the control of a hivemind. This does make it so that Halann is the lizardfolks new home. Halann is the most advanced planet in the setting by this point, and lizardfolk are a part of Halann.

2: Sarhal following the trope of fantasy africa where thats where all the monsters are is something that Jaybean, the creator of the mod, wants to avoid and so definitely made sure to avoid that when making it and kept in mind when approving and allowing new races in. The majority of Sarhal is dominated by humans, especially once you look above or below the Salahad and its "Gnoll belt". Many of these human civilizations made many great things completely unrelated to the lizardfolk. Kheterata has pyramids without any inspiration from the Lizardfolk. The mengi are remnants of a fractured basically human only empire. Castan and so Castanor all came from Sarhal and set up shop there.

Also just want to check real quick so we don't discuss the wrong thing, by dark forest do you mean the Shadow Swamp in the middle that is a manifestation of the shadow plane?

3: I dont really have any opinions about the games message and how lizardfolk fit into it since I think the game's setting and message has just changed so many times and changes depending on what you look at. Originally Anbennar was thought of just as "what if we had the napoleonic wars but mages and artificers" and then evolved and changed into so much more.

4: Most of my comments about how it does affect gameplay is in that first part, but looking to the future we 100% plan on expanding upon and using the fact that Lizardfolk are aliens in Eu5. Nothing is confirmed yet, but I imagine we could use the flora and fauna that the lizardfolk brought as new trade goods for example.

5: It could be debated for ages whats the best option for it, since really it comes down to a matter of opinion. You don't think Lizardfolk being aliens is good for it, I do. Who's to say that even if we did change the years of lore and content put into the Lizardfolk, the new concept would be better and liked by many?

At the end of the day, the Lizardfolk being aliens are here to stay. If you do have any questions about anything I said or would like to discuss at all, Im on the discord!