Sounds like it would work, I still think mounting the rails to a piece of flat bar that you have some either sloted or oversized holes that is mounted to the top of the frame tube would be a better option. Wouldn't be much more much more work since the way you want to do it you are drilling two holes anyway for the through hole and I guarantee you will have a tough time getting the top hole to line up with the bottom hole since the drill bit will walk on you since you will be drilling it by hand. If you use a piece of flatbar you can drill it with a drill press and tap it off the machine, also by making the holes that you will bolt to the top of the square tube oversized/sloted if you have some tapped holes on the tube a little bit off you will have plenty of adjustment with the rails mounted to the flat bar to still get the rails parallel to one another. Hopefully this makes sense, if not I can draw something up for you when I get some time.

I'm thinking about doing the same thing but also adding set screws so I can level the rails with out the need for shiming, with doing it this way you can get it parallel and level in x and z with out the need for shiming material just a hex key wrench. I'm confident it will be better than what we currently have going on with these machines lol. Look at the glass as being half full and that anything you do will be a improvement over it's current state, even using it as a engine stand if you choose to.