I just built a beacon with a full iron pyramid (9x9 base) at the bottom of the End, with the lowest tier at the very bottom of the map. Instead of unlocking all four levels of beacon effects, it only unlocked the first three, leaving the level II and regeneration effect unobtainable.

I don't have time to properly test this at the moment, but I suspect that the bottom-most tier of the pyramid isn't being registered correctly by the beacon when it's at the very bottom level of the map. Will report back if I can find the time to test this.

Attached is a screenshot of the beacon gui showing the top-tier effects grayed out and inaccessible, and another screenshot showing my F3 coordinates while standing on the bottom tier of the pyramid with my feet at y=1.