You need to set the lod to 0 and choose to merge materials (not on by default)
Single mesh with multiple mats:
Left mesh after merging materials:
Unreal generates an atlas like this for the merged variant:
It’s not perfect as it physically repeats the texture inside of the atlas, but to get the atlas you want you probably need c++ at that point.
Edit:
Have a look at this thread regarding tile-able atlases
Using this type of tile-able atlas along with vertex colors to define the material lerp you can get this
This gives
vertex color for mesh
1 texture only for the mesh
The x and y of the vector next to the texture coordinates dictates the amount of repeats in X and Y of the tileable texture.