I had the same error as you!
I had previously run into this error during stage 3 of the upgrade process and followed the advice suggested by unman which involved resizing the space allocated for dom0.
I am not sure if that had something to do with this failed to locally activate thin pool error that you’re describing occurring later on, but I was able to fix it with your suggested methods!
I got the warning as well and it also said:
WARNING: Sum of all thin volume sizes (<1.1 TiB) exceeds the size of thin pools and the size of whole volume group (<475 GiB).
WARNING: LV qubes_dom0/vm-pool_meta0 holds a backup of the unrepaired metadata. Use lvremove when no longer required.
I am not sure how the sun of all volume sizes could be that large as my SSD is not even 1TiB large. Furthermore I don’t know how or on what to use lvremove but just as in your case, even without doing this, everything ended up working.
I would appreciate some further insight however, if anyone understands or knows more about this!