You are making the Z axis much heaveir than it needs to be with this arrangment by having the motor, ballscrew, bearings etc moving with it. All it's doing is creating more work for the motor and lowering performance and add's nothing to the strength.
Also I would widen the bearing and rail spacing to give more stabilty, I understand your chasing space but a few CM's makes a big difference and is worth losing sometimes.

Regards the tubes, you do realise Tube doesn't have sharp edges don't you.? At this size they will have between 8 to 12mm radius and you show the gantry ballscrew bearing at the edge and this won't work as you'll be drilling into the radius and the side wall.
Yes, small detail I know but these make a big difference and are what catch you out. If you are going to model the design make sure you model every detail because if not then at some point you will find things that don't fit as you expect and sometimes they can be very diffcult or impossible to correct without major upevil.

The gantry need bracing where the bearing box meets the gantry box and again I would widen the bearing spacing.
If you are going to weld plate to the box section then only weld it in short sections 30-40mm in length spaced 100mm apart and staggered on each side, don't fully weld the edge because it will put stresses into the tube which will release when you have the tubes machined unless you have it heat treated first.

If you don't want to go the heat treat/machined route then think about using epoxy metal putty on the surfaces and putting on a surface plate to create flat and parallel surfaces. You'll need a large surface plate but it works very well and is easy and quick. I use this method all the time and it's very accurate and strong.