The transformer was chosen by the 9VAC output required and the >2500 ma current. The toroid is overkill, but will not get hot either and the magnetic field produced will be small. If you put one box on the other, you will get a tiny ticking hum, not really audible.
As for cutting the holes, these die-case boxes are extremely easy to work. I just use a coping saw with a thin metal-cutting blade. Cuts like butter in any desired shape. Drilling is also clean and burr-free, with little chips.
I used the XLR input on the DAC rather than the power plug because I wanted the option of connecting ground to the box as well. To disconnect the XLR connections, just remove the two SMT capacitors and jump over to the power connector. The XLR's also hold-on tighter than the power jack and they are cleaner to terminate. Notice that I twist all wires that have currents running in opposite directions. This lowers the inductance.