If I was bolting my pier down, would I follow what the compass seemed to indicate was North, or Just go by Polaris?
Absolutely, definitely, positively, 100% go by Polaris. Ignore that bloody compass! It might be inaccurate, your local magnetic declination may or may not match the computer model due to local conditions, and it's not so easy to sight accurately along that short needle, anyway. Polaris sits within a degree of the rotational axis.
Yes, you can succeed with a compass, but I'd double-check that against Polaris, anyway.
Your compass senses the Earth's magnetic field, and so points toward the north pole of the magnetic field, not toward the rotational north pole. And it's rotational north that you want to use to align your pier, obviously.
The north pole of the Earth's magnetic field isn't anywhere *near* the rotational axis. It's somewhere in the ocean off northern Canada and right now is sliding around fast enough to see (it's movement is irregular, but it has moved as much as 25 miles in a single year, which is 15 feet an hour, or 3 inches every minute). A hundred years ago it was at latitude 70 degrees, 20 degrees from the rotational pole! Even now, it's at about 80 degrees.
But it's more complex than that, because the magnetic field is not a nice, smooth, spherically-symmetrical thing. The north magnetic pole is at about 110 degrees west longitude rignt now, or essentially due north of my observatory. So a naive model would indicate that my magnetic declination should be close to zero. But instead, it's about 10 degrees -- and something in my environment adds about two degrees to that (assuming my compass is accurate).
Anyway, you're an astronomer, so you shouldn't be afraid go go outside at night and look at Polaris!