One of the desk units will have the computer in it, and the other may contain other electrical equipment that may get warm, so some ventilation is needed front and back.
I don't want holes to spoil the front, so I've arranged the base to stop a couple of centimetres short of the door, leaving a gap that can't been seen from the front unless you get on the floor and peer under the door. Cunning, eh?
At the back, I decided to make one big rectangular hole with rounded corners, giving good ventilation and easy access for cables.
For the first unit I used a wood drill to cut the rounded corners. This made the MDF rather too hot (not a nice smell), and the results weren't particularly neat, but after applying a bit of wood filler in a few places, then sticking on veneer edging, it wasn't too bad. And it's at the back so no-one is going to be inspecting it too closely.
For the second one, I used a forstner bit in the router to do the rounded corners, which still made the MDF too hot, but gave a neater result.
I cut the straight edges roughly with a jigsaw, then neatly with mutiple passes with the router. This took a long time to do as each line required a straight edge to be clamped in place first, and I couldn't think of a way of doing this accurately other than trying it with the straight edge clamped too far away, then measuring the error and adjusting the clamped straight edge. Tedious, but it worked.
Dowels were used again to fix the parts together. The base is raised up by 40mm as it has a small "kick-board" at the front edge, so it was not possible to use the dowel jig for the holes for this. So instead I measured carefully, then drilled as straight as I could without the jig, and it all fitted together just fine: