Nothing will happen if you weld carefully, tack everything together, don't make stitches bigger than 5cm, use your brain to figure what to tack before so it would not twist and most of all be patient. It really takes a lot of time welding a CNC frame.
What you suggest is alternative but people go further this way and don't use epoxy at all / only at the shims/

Anyway, most of all you should care for your top 2 rails to be more or less in the same plane. On paper the epoxy to spread the force needs to be minimum 3mm thick, so basically that's your limit. You can pour more than 5mm if needed.