Is there a reason that you don’t want the two varieties grafted to one tree? If I had a small backyard that is what I would opt. for.
But back to your question, it shouldn’t really matter what root stock they are on as far as them being planted next to each other. The main thing (in my amateur opinion) that I would be concern with is my soil type and climate verses the soil and climate needs of the root stock, the disease resistance of the root stock and the suckering habit of it (I wouldn’t want to deal with suckers like this from a recent thread.)