I say the time determination and spot determination are separate issues, and here's why:
The reason for the provision stopping the clock on out of bounds was because of the extra time necessary to return the ball to play from farther away. Yeah, it's not much farther away when the runner takes just that extra step to go out of bounds, but they drew the line somewhere. I suppose they could've applied the same rationale to balls dead in a side zone, returning it to the hash, but they didn't.
The reason for allowing forward progress in determining the spot was to avoid a prolonged mauling of the runner by the defense to improve their spot. It was possible for the runner to yell "down" if he chose not to be pushed farther back, but the officials didn't like being in the position of recognizing whose voice was saying that, so even though they retained that option in the rule book for a long time (only NCAA having eliminated it so far
AFAIK), it wasn't exactly encouraged when forward progress was put into the rules.
Certain means by which the ball becomes dead are sufficient to determine clock status, but not to determine the spot for the next down. They're separate issues, connected only in some cases. When someone carrying the ball is carried or thrown backwards by an opponent, the ball can still become dead by any of various means, and even the
time the ball becomes dead is not determined by when that player started to be carried or thrown backward. You wouldn't put a second or more back on the clock because that time elapsed between when the runner started to be pushed backward and when his foot hit the sideline, would you?
Robert