Hi Gregor,

Looks nice and sturdy and there's no reason why you can't use 50x50x40 but I would say if you haven't already bought the linear rails then don't buy round rails.
Profiled linear rails have really come down in price in the last year or so and it's not worth buying the round type IMO. They simply don't compare in performance and accuracy.

Get the rest of machine designed then well take another look. Don't forget to think about cables runs and Home/limit switch mounting etc.