The old rules were clear that the score should be called/time starts to run immediately
after the ball went out, and for the most part that was the case, so your contention about similarities between the new and the old situation is misplaced.
If the umpires did something different, it didn't affect the perception of how much time has passed (unless in extraordinary circumstances, but that is an exception), as the rules were clear about when that happened, and the umpire had no influence over that occurrence.
Finally, to the last part of your post: Nadal will have to get in line, otherwise he is getting a bunch of violations", and then some more.
However, Nadal is not stupid that way. He knows exactly that the new rules put a stop on his intentional stalling on crucial points, so he needs to conform to the new rules.
If we don't see him sanctioned often, it will be because he was forced to play by the rules, not the other way around.
The current rules are designed to give the players more time (thus validating the old situation), but will stop them from stalling intentionally, and since the Nadal fans claimed that the only reason why he does it is to have a bit more time to prepare himself, they should be extremely happy with what he got.