The problem with your two designs, is that in the 2nd design you still don't have more movement of your Y-Z axis assembly as the Z axis is lower than the gantry tube and will still contact the plate.
That is a slim profile for anything but a small length gantry intended only for wood at low accelerations. Of course if that's what you're doing, and you're sure it will meet your expectations, then forget I mentioned it. It is possible to bolt some square steel tube to the unused face to make it stiffer. That's a cheap and easy stiffening technique for T slot, but perhaps not the best.
Many designs that use more than one spindle have extended length tubes for more movement because the the wider Y-Z axis assembly from using two spindles. Perhaps look at some of those designs.
My personal preference for a moving gantry is to have the front bearing at least as far forward as the cutting bit. For a fixed gantry, the angled support can go in the other direction because you don't care as much about the weight and you can make everything stiffer, but those are just my opinions. Like I said you can do some searches to see what multiple spindle designs typically do and that might help you. I believe you would have a cut out where the spindle can pass the uprights, and the front bearing is still forward, but the uprights are typically made of a box type structure for this to be more rigid, not a single flat plate with more of a cut out in it.
The two things you have drawn will probably perform about equally. If you are dedicated to using flat plate for your gantry risers, then you could also bolt on some Heavy duty steel angle iron to the sides, that would stiffen them up.