Unfortunately flipping of text has been like this since FPSC and has remained ever since to allow backward compatibility with older models.
There is two ways around this either you flip the uv map, or when designing your normal or text for the color texture have it pre-flipped.
As for dealing with multitextures.
Don't work with blender so I don't know. What I normally do is export the unmerged mesh to llithunwarp, assign each uvmap a texture slot, import back to the model editor, assign the textures, then merge the mesh export again. Import into fragmotion, and assign the textures again and export, correcting the normals/smoothing ect, export as an object file and job done.
Use the import function in max and that automatically picks up all the textures and assign them, without having to lift a finger due to the ground work being already done, having the textures referenced in the model it self.
Manually trying to assign via FPE isn't going to end well, if the model file doesn't correctly reference the model. So you would need to change your work flow and make sure the the model file references the textures correctly.
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