What happens when the operator is called from another operator which also called to_mesh on some objects, but which should remain valid when this operator is done?

That is a good question, current design for freeing the meshes is done via obj_eval.to_mesh_clear() afaict -- introduced in rB32d5d127cb49. meshes are outside of main, owned by ob, cannot be removed from bpy.data.meshes...
Afraid I have to pass this question on to @Sergey Sharybin (sergey)... [not sure if above usecase is supported still... worst case scenario: create them again in the other addon?]

Oh, hold on, should we be using bpy.meshes.new_from_object() instead of object.to_mesh() then?

Like D5114?