Alright, over the past hour, I invented a new warcrime by reloading the save right before Alla gave birth, forcing her to undergo labor dozens of times to give birth to all manner of otherworldly mutants, in the name of Science. Here are my findings.

I am 100% certain that the bug is caused by this mod: Specifically, when altering its mod options for the player's own faction type (in my case, PlayerTribe) to be anything other than 100% vanilla and mod-added xenotypes (hereafter called "Old xenotypes"), or more than 0% Hybrid, Random Genes, and custom xenotypes made by the player (hereafter called "New xenotypes"), any newly born baby may or will have a New xenogerm.

My experiment was simple: Change this mod's settings for PlayerTribe, reload the save right before Alla gives birth, and note the baby's xenogerm after it is born. I found that it makes no difference if the settings are changed before or after loading the file, only if the settings are changed before Alla gives birth.

When I changed the settings to guarantee a New xenotype, Alla's baby would be bizarrely altered to become the promoted type of New xenotype. When I set the settings to 100% Random Genes, Alla always gave birth to a new type of xenohuman I had never seen before. When I set it to 100% Toxoid or 100% Photoan (two custom xenotypes I made and saved), Alla always gave birth to a toxoid or photoan. When I set it to 100% Hybrid, Alla always gave birth to a hybrid seemingly combining the genes of two Old xenotypes.

However, this was not true when changing the settings to promote Old xenotypes. In that case, Alla's child always had the xenogerm the "Inspect baby genes..." button said it would; a baseliner with mid-black hair and light skin. When I set it to 100% Sanguophage, Alla always gave birth to the expected baseliner. When I set it to 100% Impid, Alla always gave birth to the expected baseliner. When I set it to 100% Saurid, Alla always gave birth to the expected baseliner.

In conclusion, there is definitely something off about the way this mod handles childbirth and New xenotypes. I can speculate a bit about how this mod works: Whenever a new pawn (called "Alice") is created by an event (such as raiders, caravans, drop pods, or childbirth), the mod checks Alice's faction type and creates a random number. If the random number is above a certain value N, and the mod settings specify that Alice's faction type should have N portion of xenotypes, it replaces Alice's genome with that of the specific xenotype. There might be a check in place to make sure this process doesn't complete if the event that created Alice was a childbirth. However, this check only works in suppressing Old xenotypes, and doesn't work with New xenotypes.