Well, this is common for every wiki, too.

What I say is to have different settings by family.
Either using command line parameters or modifying user-config each time is uncomfortable.
For the individually developed script that runs in my local wiki only, there is a solution: copying
pywikibot.put_throttle.setDelay(delay=0, writedelay=0, absolute=True)
into each script. That's not nice either. But is not good for framework scripts.
Families may have different needs. I can easily imagine a wiki where the majority of edits is done by bots, and humans make less contribution. Sleeping is not neccessary. Nor in a low traffic wiki where nobody is disturbed by bot work. WM Foundation's server farm needs the maxlag conception that is unneccessary for a single server wiki.
It's good to have a basic setting, and we should have an optional config setting for families that overwrites default.