I separate the sauce and pasta for a different reason: I cook a large batch and will always have leftovers, so keeping them separated prevents them from spoiling faster (even when refrigerated). An already-mixed spaghetti also gets dry in the fridge compared to heating them separately later on.
Heating them together is usually fine in my experience, but storing them separately is a must. The pasta robs moisture form everything else, getting mushy and leaving the sauce dry.
If you really want one container to bring leftovers to work, put the sauce on the bottom add a layer of cheese, then put the pasta on top. Don’t mix everything until it is warm. You can get surprisingly ok results this way.