The edges with aluminum will leave a lot to be desired, but it isn’t hard in a metal shop to clean them up nice with a grinder and sander. I have gotten steel to have decent edges by playing with the plasma cutter’s power and the feed rate. I have only done a few cuts with the Torchmate, waiting on more scrap to play with before actually buying good stock. People that get them dialed in can get pretty good edges. Not waterjet good, but waterjets are many times more expensive than even a large cnc plasma cutter.
As for the holes I would redo the cad drawing before importing the dxf into the software. With small holes I would just make them points to get a pilot in the right place then drill them out. You could make a jig pretty easily to gang drill them or just hold them steady for one hole, drill one of the holes in each plate, then shift it for the other hole. That would take a while though. Once you got into a grove you could still do it cheaper than water jet unless you value your time very highly.
The machine I run maxes out at 2ft by 2ft, so you could fit 6 vertically and 7 horizontally so 42 in one 2×2 sheet of material, assuming autocad isn’t giving me weird dimensions. The cut would take a few minutes, but you wouldn’t have to be totally babysitting it. You could be drilling the previous batch or cleaning up bad edges.
I will make this one of my practice cuts next time I get scrap about the right thickness and see how good I can get it to turn out. I might end up making them from steel since I haven’t printed them yet anyway.