A typical z axis has a rail that is fixed to the x axis and a gantry cart that moves the spindle up and down the rail for the depths. Would it be feasible to reverse this and have the spindle fixed to the backside of the rail and the gantry cart fixed to the x axis so the entire rail moves up and down? My concern would be any flex that would result from gantry card. Another thought was a double wide gantry cart where the spindle is attached to the lower part of the plate but the wheels are attached to the upper part of the plate so the spindle can progress lower than the bottom the rail. Once again, the potential for flex in the plate would be my concern here as well. Would it be much easier to have longer vertical rails on the side and just adjust the horizontal rail up and down those vertical rails if more or less height is needed? It isn't that often that I would need more height for the z axis but it would be nice to be able to utilize my CNC for the completed product and not the components.
The issue you’re not seeing here is that when you go with the moving Z-rail, you have to set the lower X-axis rail higher to have additional clearance due to the bit and spindle protruding down below the Z-axis gantry. This raising up and then reaching back down inherently reduces the stiffness of the system so you’re losing ground from the getgo. We’ve learned this from 10 years of trial and error here. The easiest solution to your problem would to fab a taller gantry plate and run it on a fixed axis. As for adjustable verticals, it’s doable but you risk messing up tramming every time you loosen the sides. Taller also reduces stiffness. Removable sections of the spoil board may be a better solution to increasing available height