It seems like that add on just creates a bunch of extra geometry by default - the top faces are subdivided strangely so even creating an vertex group of only the top faces and using that to select the extrusion still doesn't fix it.

I just ended up scaling the z to 0 and doing a limited dissolve to get a single face per island. Then the geonodes set up behaves as expected. As long as you don't specifically need that extra geo it should be fine right?

[<img src="https://blend-exchange.com/embedImage.png?bid=YwYxVWXX" />](https://blend-exchange.com/b/YwYxVWXX/)