focusing on code size is possibly misleading

It's not the best metric, but it's close enough in this case. The whole problem is that large commercial (and some open-source) systems are in the millions of lines of code. What is all that code doing?

code size does not exactly equal orthogonality

One implies the other, at least in the way they've phrased the problem. Their goal is to build everything using only 20,000 lines of code. This means they have a strict overall budget and therefore cannot afford any duplication anywhere.

They weren't required to change the stack

You can't go from millions of lines to 20,000 by making incremental changes. The whole system from the ground-up has to be rebuilt with the code budget in mind.

they should have waited until they hit beautiful enough technology that would require such a change

They would be waiting forever. At some point, you have to dive in. Nothing good ever gets built without several iterations. Combine this with the fact that frameworks and languages are best built simultaneously with the applications that will use them (so that the levels of abstraction are correctly tuned), and I think their approach is perfect. By being forced to consider all levels of the stack, they achieve all of these goals.

Incidentally, they're not hoping to get the system built in one go. They're "building [at least] one to throw away", as Brooks said. They are building a rough version of the system (over-budget on lines) to see where the problems are. Then, they will use this first system to build the real thing.

At its heart, this project seems like an ideal way to do research into computing systems. Take on a daring project which will require many innovative ideas -- some small, some large -- while making sure that you're always tied to reality by having concrete goals and need to have some sort of a working system at all times.