Probably because you are usign flat shading instead of smooth shading. Normals at 90 degrees are split in engine.
Edges marked with the UV map seam is split in engine, UV maps is only a tool that exists in 3D software that doesn't break loops, in engine the mesh is split at that seam.
A second UV map as used for shadow baking also splits the mesh where it's edges is.
Smooth groups, Sharp edges and Custom normals will split edges; causing more vertices.
This isn't some kind of bug or even a Godot thing, it is how graphics cards work.
As far as the engine is concerned UV maps, Smooth groups and Sharp Edges are all just splits in the mesh and it has to make 2 vertices at those points.