I've always found the fixings naturally sit low in the slots. When I've tried to jack things up before securing there has not been any indication that you can achieve much and nor does it seem necessary for any alignment purpose.
I don't think you want the box resting on the support because that nullifies the purpose of the rubber mountings, so I would try to adjust, if just a little bit.
I don't think you want the box resting on the support because that nullifies the purpose of the rubber mountings, so I would try to adjust, if just a little bit.
I agree ^^ , but as regards adjusting the gearbox, I'd suggest fitting spacers between the mountings and the support - these could be easily fabricated by drilling a 5/16 inch (8mm) hole in some 1/8 inch (c. 3mm) flat steel, length and width to match the rubber mounting metal plate. Alternatively use a couple of large outside diameter (penny/mudguard?) washers as spacers. There seems to be sufficient remaining thread on the mounting studs to insert spacers totalling 1/8 or even 3/16 inch (3 - 5mm) each side. (you need to have 1-1/2 threads protruding beyond a self locking nut for it to be secure).
Using spacers in this way might also stop the distortion of the rubber mountings evident in your 1st. picture - this tends to peel the rubber away from the backing plate over time. Just don't overdo the packing or you might find the gearchange rod starts to bind where it exits the tunnel.
I reckon that c.1/4 inch (6mm) clearance between the gearbox casing and the support bracket should be sufficient.