If I install using

pip install -r ./requirements.txt

then pip installs the packages in the order of the requirements file.

Actually this is not how it works, pip will install in any way it sees fit, and it is not consistent between versions (it has to do with dependency resolving)

However, during the installation process from ClearML, it installs the packages in order UNLESS there's a custom path provided, then it's saved for last

Correct because the custom (I'm assuming you mean install from git) package might need some of the wheels

The entire reason why I have the custom versions of the packages is I had to manually resolve a conflict between the darts package and hydra/omegaconf (hydra is working on an official solution but progress is slow).

You can configure the agent to first install specific packages, and only then others, just add the package names here:
None

I guess I could build a container.

always a good option