The point in actually enforcing the rules is not to punish people for the sake of it but to discourage from such behaviour. When red cards were handed out for studs-up challenges, did we see fifty red cards per weekend or did we see fewer studs-up challenges?
If players were booked for tackles that are prohibited by the laws of the game then they’d stop doing them after a few weeks and a couple of red cards. They're not amoebas who can't adapt to being called out for trying to bend the rules to gain an advantage on the pitch.
The refs are in charge of making sure that the players play within the laws of the game, not to ensure that the game isn't stop-start. And how much more does it stop a game to pull out a yellow card when you've already blown the whistle and stopped play? It ensures that the same player isn't going to commit 4-5 more fouls in the game (unless it's Matic because then you're off after three fouls obviously) and actually improves the flow of the game.
However, the refs need to be brave and actually send players off for these things if they get specific instructions to do so (which they haven't yet, despite media picking up on tactical fouling). A few years ago, they were told to stamp down on dissent. In the first few weeks we saw tons of yellow cards for dissent, but they never followed through on it because they let players off for incidents later on because they'd already been booked. During those weeks, Diego Costa was booked for dissent against West Ham. Later on in the game he made the tackle below on Adrian and didn't get a second yellow card, so it was all for nothing anyway.