[aetimmes]

Assuming based on GP that this is in a HPC environment, there is often a delineation between the people writing HPC software and the people maintaining the clusters and the software installed on them. Telling a brand-new graduate student with zero software development experience to just throw everything into a container results in running code that is not optimized for the hardware it's running on, which in turn negatively impacts the other users competing for compute time on HPC clusters.

There is a movement to incorporate technologies like Singularity into the HPC workflow but for established projects, it often looks like a lot of bikeshedding for negative results compared to just running the code on bare metal.