I ended up spending a fair chunk of my balancing time poking the DMs I know to get their read on the cover penetration property. The consensus was that, while cover penetration can be juicy, cover penetration on a polearm is only useful if Your DM likes to incorporate clutter into their battlemaps.
I went the route of making it penetrate a set thickness of all cover, rather than having it outright ignore half/three-quarters cover, in order to differentiate it from things like the Sharpshooter feat. There are pieces of half/three-quarters cover that are thicker than 2 feet, and pieces of total cover that are thinner than 2 feet, and I thought that nuance was worth capturing.
Of course, being able to stab through (thin) total cover doesn't help you aim through total cover (or any other cover, really). The easiest way to capture that mechanically is to treat all cover as if it's one tier lower (total as three-quarters, three-quarters as half, half as none) but that approach won't fit all situations. You'll have to play it by ear.