The issue was caused by the msi transform location noted in the registry (a temp folder), which no longer existed.
The fix is just to clear out the Transforms key contents in the registry, which forces the Windows installer to use defaults instead. See a similar article on it here.
Next up, the TSE who couldn't help me with the first issue, suggested that I use SSO credentials for both parts of the vCenter install. This failed right at the end of the install phase, and after automatically ripping out all the v6 components, I had to restore my vCenter from backup.
I strongly advise using local Windows administrator credentials for this part. I did that and the rest of the install worked as expected for me. Hope this is of use to someone else searching for the same problem.
