For pause - F11, P and middle-click are all assigned Pause by default. The last one in particular I have noticed is very appreciated. Prior to remappability, all three keys were hardcoded to pause for quite some time; including middle-click remaining hardcoded to pause when keys were remappable but MMB/RMB weren't.
In many cases, the reason for the NL defaults are "these were Lemmix's defaults". Some were proposed (eg. Z/X for relative skill changing), others were a matter of "where's a free key for something that doesn't have any obvious key" (~ falls into this category).
For reference:
http://nordicbots.com/?id=73&net=quakenet&cid=84924&year=2016&month=3&day=6Discussion on hotkeys starts at around 21:37.