Am I the only one doing the in-place upgrade (manual at the moment) where the process didn’t convert qubes-contrib-vm-r4.2.repo, both the file name and the content to 4.3?
So I have to manually edit the file in each template in order to upgrade it to 4.3.
I have no idea if this happens when using all-pre-boot and all-post-boot
If I am the only one, what could I do wrong executing each STAGE manually?
You should be able to rerun the stage 4 (--template-standalone-upgrade).
The tool already allows you to run each stage manually 
It looks I wasn’t clear enough.
Manually running each STAGE doesn’t invoke renaming stated repo. I have to manually edit it in addition. For all other repos, the process of repo upgrading to 4.3 repos is automatic, when I manually run the STAGE.
It is easy to check. Did you have named repo 4.2? If no, you probably don’t know what I am taking about. If you DID have it, was it renamed automatically to qubes-contrib-vm-r4.3.repo and in it all he repos replaced to 4.3, or you did it manually afterward?
I guess yes, the dist-upgrade tool code only converts the main .repo file, leaving the contrib repo file alone.