According to the documentation, when concurrent package options and command line options,
always package options are used.

I think in case of rerun and of runall this is not appropriate.
If i run a command with command line option I want to beat internal options.
maybe also worth a consideration: the stricter option shall win.

In my case i want to run latex and pythontex in a way that it is really reproducible within an environment.
So I shall have rerun=always.
Of course, in other contexts I want to be fast, so I put rerun=modified in my package description.