I wear mostly PvP pieces, and use some PvE armorings in my belt and bracers, and power crystals in my weapon / offhand. So, I agree that PvE gear isn't across-the-board best in slot.
That sad, that mmo-mechanics piece is a bad article (besides the fact that it's old and doesn't take into account the new gear). You can't examine the effectiveness of a particular stat (one that the hybrid set has less of by definition) by just saying "Here is the damage / mitigation / healing you lose by wearing the hybrid instead of the full PvP set". You need to compare the expertise sacrificed to the stats gained. For instance, by swapping out my crystals, I gain one power and lose just one expertise - this is almost always the right answer, but is especially correct when building a smash Jug / sweep Guardian.
Also, I believe you're building up a bit of a straw man here - I don't really see anyone claiming that a full PvE set is best for PvP. Most people seem to be trying to trade expertise 1:1 (or close to it) for regular stats when they can, especially when they're further along the expertise diminishing returns curve. That piece only looks at Battlemaster gear, and doesn't even go beyond 1200 (my expertise is over 1200, and like I said, I have PvE armorings in two pieces, and two crystals swapped out).