I don't think this play deserves a special enforcement as "something not covered in the rules."
None of the 3-4-3 AR's in the current book suggest that time can be put back on the clock. Instead, they address whether to go on the start/snap after a team has obviously fouled in order to conserve/consume time. And most important, in the ARs, the offending team is taking advantage of a situation in which the offended team is powerless. (Delaying the game when the ball is dead, jumping offside, etc.)
But keeping a live ball live is different, in my opinion. In the play in question, Team B needs to conserve time. And they can do something about it (unlike the offended teams in the ARs). They can have someone back there to fair catch the punt. Or field it and return it.
If the ball bounces near a sideline and Team A bats it back into the field where it rolls around for 5 seconds, are we putting time back on the clock?
Or let's even say Team B does a have a return man, and Team A commits KCI, after which the ball bounces/rolls for 8 seconds. Are we putting time back on the clock??
Of course not. Granted, those scenarios aren't as "obvious" as the original one. But the original play, while obvious, isn't obviously unfair in my opinion. Team B opened the door to a time-consuming bounce/illegal touch/illegal kick when they didn't take steps to conserve time.
I do, however, think that the clock should be stopped as soon as the ball comes to rest. Team A shouldn't be allowed to breathe new life into it by kicking a motionless ball. But until then, if Team B wants the clock to stop, they can down the kick.