Important to remember that option (c) has TWO requirements: legal kick AND a new series. If you have a punt that's brought back for a penalty that backs up K, clock starts on the RFP.
Also, for Mad Mike: you'll notice that COP is not on the list of major clock stoppers that you quoted. Here's a play that shows why:
PLAY: Runner A1 fumbles, and B1 recovers and begins to advance. B1 then fumbles, and A2 recovers and is downed.
RULING: New series for A (5-1-3d). But clock will start on the RFP (3-4-2).
The rationale for starting the clock on the snap rather than the RFP is to allow the teams time without the clock running to swap out offense and defense. In this play, obviously that won't be necessary.