I’ll see to add a mention about symlinks in the text.
Note that flit does support .pth too, and the flit POC linked in the initial post is based on that. It works just fine, especially with the src layout that flit now supports too.
As a side note I do have a requirement to use symlinks in a custom backend and I could implement it with PEP 660 by generating the symlinks on interpreter startup (via an executable .pth that is put in the wheel by the backend). It is a not particularly elegant, but I just wanted to note that it is possible today.