It seems the output path option only changes the name of the object being generated not the dist path itself.

I assume you're using https://www.pantsbuild.org/docs/reference-pex_binary#codeoutput_pathcode - which is the right idea. If you configure:

[GLOBAL]
pants_distdir = "%(buildroot)s"

Then you should find:

pex_binary(
    ...
    output_path="foo/bar/baz"
)

Nets you a PEX file

baz

at

foo/bar/baz

in your repo after running

./pamts package ...

on the `pex_binary`target.