If I create a document with text anchors and then make an alternate layout, InDesign gets confused as to where the links should go. I would love to be able to create the alternate layout and have InDesign understand that those links go to the locations in the newly created layout.

Apparently, the broken text anchors in alternate layouts have been an issue for a while. Here's a thread on Creative Pro (https://creativepro.com/topic/text-anchors-in-alternate-layouts-broken/) from 2013 about it.