Another point that seems related is the difficulty of call/cc semantics when dealing with changes in state that are outside the semantics of the virtual machine. It seems to me that there is no easy way to avoid cases like described in the article without forcing explicit accounting of a massive amount of implicit state. Depending on your use case the tradeoff might not be worth it.

On the other hand, I would argue that the idea of a build is an entirely valid and useful construct, it merely represents a point in state space against which test cases (and production) must run. It is impossible to get away from that state. Some tools can make managing it easier, and some make it virtually impossible to manage. Imagine that we discovered a magical halting oracle and that we could compile everything instantaneously, we would still have to figure out what combination of states were valid, and we would call that the 'build'.