Without getting too much into spoiler territory, it seems that Monkeywrench is either written oddly or was originally intended to be a longer scenario.
[ Spoiler ]
Specifically, the initial run is described as being a "dry run" for Phrex's escape from Horizon, but the actual mission seems to imply that it *is* the escape; the test for figuring out the purpose of the wiring job mentions that it allows Phrex to access the Ares network, and the debugging section says that Phrex will use the hole in the floor to jump into the Talos drone.
Ultimately, I suppose that it doesn't *really* matter (since it's more behind-the-scenes stuff rather than being integral to how the mission plays out), but I'm trying to wrap my head around it.