That's really unfortunate. It appears to have been substantial damage. I hope it can be repaired within the often rather tight budget constraints of the Arecibo observatory. This radio telescope deserves more funding!
Is Arecibo doing 1st rate astronomy still? Is it likely that there will be a huge call (or justification) for funding to repair this quickly? Versus spending the $ on other students/research programs? I wonder how much the $ bill is -- maybe on the order of <$5M?
I don't think any are intentionally different heights. Part of it could be the thing was built nearly 60 years ago but also it doesn't need to be perfectly accurate to securely be tensioned.
I would bet they had a standard construction form (2 meter tall Sonotube, etc) and they simply dug down until they reached the rock and poured the concrete. Like you say, they height doesn't matter since it will be referenced from some other datum.
My guess: currently used as towing points to tension the parabolic structure. You can see some wires in the picture. And probably also a helpful structure during construction.
That makes sense except for the irregular height. If they were all the same, or even if they were roughly parabolic themselves it would make more sense.
Perhaps it's an optical illusion. This photo seems more regular and confirms the tie-down aspect (I'm sure it's how the curvature is maintained).