I found the solution for my issue at least: if someone stumbles upon this having similar issues:
If you draw your merge from an LOD > 0 then it can happen that all triangles sharing a material slot got removed and thus the material slot got removed therefore the mesh merger gets confused when he has to assign the materials and bake them and this will result in the merged result having the wrong materials baked into it. Solution: morge from LOD0 and then reduce it (usefull for proxy mesh workflow)
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