It's better to add a custom target and set the dependencies on it so you don't run the command every time.

You may want to look into src/test/data/generate_header.py and how it is used.

There are no dependency on hexdump. I don't understand why the approach taken by src/test/data/generate_header.py is not preferable.

The dependency exists as long as autotools is still supported, the script is just the direct translation of the Makefile.bench.include scipt (only special autotools variables names are adapted).
That said, I don't think the generate_headers.py solution (translation of the bash script to a python script) is worst, it's even a better long-term solution as it effectively removes the hexdump dependency when autotools support gets dropped. I will do the translation.