Spell penetration in PvE is garbage. For frost it seems to have no effect whatsoever; for fire and arcane you have a 'phantom' 5-15 (depending on mlvl) points of resistance that can't be overcome by any means. Additionally most mob passive resists will be wiped away with Curse of Elements/Shadow anyway, though again the 5-15 phantom points will always be present.

It's useful for PvP against a target with splash resists but less so for a target with concentrated resists.

It might be of slight use in trash where not all mobs will have CoE on it but that would be it.

Sometimes CoE isn't up on the mob right away, say if the warlocks are busy doing something else or they've somehow gotten themselves killed. Still I try not to run with too much +spell penetration simply due to the aforementioned reasons... when you have CoE up, you pretty much don't need any.

I've yet to encounter raid mob with any amount of noteable frost resistance, so thus far penetration gear has been worthless for me in PvE. Fire and Shadow both have some mobs with heavy resists (Lucifron, Golemagg) but in many cases the mobs you care about are outright 'Immune'. It's certainly a stat they could have handled better.

Or they could just come out and tell us what it does already because all of the mechanic working in the world is telling us "this shit is useless for PvE, why is it on our T2.5 and especially T3 gear".