The Nexus 5 is extremely susceptible to thermal throttling which this article seems to gloss over or entirely miss.
Yes PVS scores do indicate something. They indicate the efficiency of a chip at a given frequency. The lower PVS numbers will heat up faster, and thus be at the optimal 2.23Ghz frequency less often, thus giving the perceived impression of being significantly slower.
I have a Nexus 5 myself, same PVS scoring (1). Running Antutu in my hand, and I'll score 22,000 - 23,000. However, out of curiosity, I rest the phone on an AC vent for 15 minutes, started the Antutu benchmark while leaving it there, and managed to score 29,500. All results easily and consistently repeatable. And my phone has never been unlocked/flashed. 100% Factory ROM, 4.4.2.
The issue purely heavy thermal throttling under heavy sustained loads.