Dear Josue,
in the moment I am on an Astropy hackathon, where we also discuss the status and future of PyVO (upstream) and to find out problems and solutions for that software. I there took the opportunity to look into the Debian package here.
One question is the handling of the version.py file. Is there a reason why this is overridden in you package? That are the two patches removes-version-generator.patch and 00-create-auto-generated-version-file.patch. When looking into the astropy-helpers code, I don't see a reason to handle this manually.
I tested this, and it seemed to work fine.