What you do and do not put into external runtimes is a matter of how you view things and your workflow.

I have a set of standard runtimes and then I have working runtimes for the projects I'm currently working on.  When the project is completed, the runtime is archived with the rest of the working files in the event I need to work on the project again.

It's also not uncommon to set up your runtimes one way only to find a year or so down the road that you need them another way as you workflow changes.