After a bit of playing, I found that the load in Phase 2 does indeed reload the Partition Boot Block and an additional 31 sectors at 0x88000. Looking at the code and stepping through execution with Bochs, I have confirmed this to be correct.
I am starting to see the structure of the Phase 3 load and it does not seem as documented. I believe this module loads os2boot and it only contains the mini-file system. It next loads os2ldr, sets up the required structures and then jumps into os2ldr.
I’m going to post my notes to the blog, link at top of the page.