If I start rotating switches in all kind of directions all over, someone is for sure going to complain that they feel different mounted in different orientations. Also it gets insanely messy =P
My work flow usually goes something like this: "Lets keep as many of the switches as possible in the PCB mount footprint." "Let me just take this hole out of that footprint, and the other one out of this one..." "It sure would be effin' great if those holes overlapped when switches are placed 1/2 unit apart, this way there will be a ton of slot holes." "Damnit, plate mounting is the **** anyways."
A lot of the footprints can certainly be made PCB mount compatible. Some locations with only one of the holes present, the other one being eaten by a larger hole of another footprint. This would of course improve something on stability, and ease straight mounting. Believe it or not, but all those small holes actually get in the way when trying to route everything somewhat neatly =P
Last, I have a question as well. If the controller is surface mount directly to the main PCB, should the diodes be SMD as well or do you think it is better to keep them through hole since all the switches are anyhow?