Actually, the PR and Driver on the same face has been done a lot and should work fine.
Aestheticly, your box will look nicer as it will be taller (Asuming a over/under shotgun- like configuration)
I've always found the driver/PR on different sides to be aestheticly unpleasing.
As for sound, the PR is reacting to pressurization of the box more than any directed force, so I don't think it will affect it in any way no matter where you place it (even on the top).
For alternatives, you may consider placing the PR or driver in a down-firing orientation, but I am not sure how that will affect things (DF requires certain specifications that I do not understand).