This is true for freeways and possibly multi lane arterials. It's absolutely not true for small neighborhood streets, which seem to be the shortcuts at issue here.
It's faster to take residential streets if the freeways are completely backed up to the point they're moving slower.
The article also appears to state that it doesn't model the load dependent throughput-- 'The instant the time penalties work out,” DwarfLord claims, “Waze will just as happily send a thousand Wazers down'. Which isn't surprising, since routing a lot of cars independently is computationally tractable but adding capacities to the problem makes it NP-complete in theory and much harder in practice.