Allow inverse of `--no-eval`?

Related to the discussion here: https://cwl.discourse.group/t/singularity-exec-vs-docker-run/956/5

The addition of `--no-eval` to singularity calls by 1557c8d some time ago prevents the on-the-fly modification of e.g. the PYTHONPATH inside an Apptainer container via something like `APPTAINER_PYTHONPATH=/my/new/path:\$PYTHONPATH` (and there is no `APPTAINER_PREPEND` equivalent as far as I know).

Preventing spurious stuff being evaluated was probably one of the intents, but for some quick development testing and dealing with fast-moving dependencies this kind of modification provided me with an easy way to test something without rebuilding an entire new container.

I was wondering if it would be possible to in some way allow the removal of this option? For me the use case is in combination with Toil, so perhaps that would need some alignment between toggles. Currently I'm removing these couple of lines manually from cwltool to "fix" this roadblock, but an official way would of course make life a lot easier if possible. Or perhaps I'm missing a better way to do this, for which suggestions would also be appreciated.