I want to inject a bash command after the repo has been clone (and maybe even after the venv has been installed).

LazyTurkey38 the created venv inherits from the system environment, so in theory you can do all the installation on the system python and the created venv will just inherit the packages, no?
(btw: just to clarify, there is only one entry point for the custom bash script and that is before everything, so users can configure the container before the agent starts)