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It's a natural part of their genetic code vs an implanted organ to mimic having the xeno genes, with that organ being implanted or replaced completetly with a new one.
Not too familiar with archite genes, I'm only fiddling with starting with them for the first time after many failed attempts to get robotic pawn type mods working.
Once on map they will also be differentiated on the hud, divided into completely separate areas if germline vs xenogerm. You can see the grey backing for the germline in a seperate category from the blue back of the xeno. Then the Fancy archites xenogerms get their own back colour. Never seen a germline archite, if that is even possible so dunno what that would look like. The other colours and shapes are just mod stuff ignore them.
https://steamcommunity.com/sharedfiles/filedetails/?id=3367770249
You also can't implant anything at germline ever, a gene is either in your germline at the start or it never will be. Only Xenogerm genes can be replaced or removed as the whole list of xenogerms are removed at once when you implant a new xenogerm. Extracted copies of germline genes will be implanted as a xenogerm as all post birth genes are xenogerm genes.
You can extract all of them slowly over the run to make xenogerms from his genes. you'll need to go down the research tree for genes to make xenogerms from the genes copies you extract. Long cooldown for extracting genes nonlethally so it'll be a slow process. Once you have them all it litterally costs nothing to make non archite gene xenogerms so you can make an infinite amount once you have them. If you put archites in it'll be much harder as you'll need a special resource. Can also buy genes from traders and collect from any colonist or prisoner with genes to hopefully speed up the process.