Have you ever tried driving 65 when everyone else does 80 (and the law says 65 mph)? It's borderline reckless to do so. All sorts of people will be passing you, creating unnecessary merges and lane switching that decreases road safety conditions.
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.