I believe the C64 keys were carried over from the VIC-20. The VIC-20 keys (somewhat at least) have some history from the PET series too.
Taken from Wikipedia on the VIC 20:
When they returned to California from that meeting, Tomczyk wrote a
30-page memo detailing recommendations for the new computer, and
presented it to Tramiel. Recommendations included programmable
function keys (inspired by competing Japanese computers),
full-size typewriter-style keys, and built-in RS-232.
The keys you mentioned are mostly self-explaining. RUN/STOP would run or halt an application and was programmable in software. The fact that "RUN" rarely (if at all) started an application wasn't a limit of the key.
The C= key could be said to exist as mere corporate branding such as the "Apple" keys on the Apple II series. Useful as a META key or "special" key to allow specific combinations in software.
I have to admit, I'm not sure of the history of the Restore key.
Also, keep in mind, that before the VIC-20 the biggest success Commodore had in computers was the PET. The PET originally had terrible calculator keys that was quickly replaced by a real, full-travel keyboard. Commodore seemed to learn their lesson in bad keyboards as many of their computers after the original PET actually had pretty good keyboards. Even their cheaper models like the C16. Of course, there are exceptions.
Finally, Tamiel was legendary in using parts he had on hand. Which is one reason why the C64 inherited the VIC-20 keyboard. So he wasn't going to design a completely new keyboard for the C64.