If there is a stop clock, it's not a big issue anymore if teams take a while to take a free kick or thrown up. So teams can start using that tactically, basically create mini time-outs. Someone pointed out that Southampton(?) seem to have done something like that on occasion this season, by creating a longer break due to 'injury' treatment. In theory, that would benefit both teams, but it obviously benefits the team most that has prepared for the situation. (For Southampton(?), there would be drinks ready and there would be a tiny team talk - if I remember correctly.)
I suppose there could be other scenarios as well, but long story short - if there is a stop clock, there should still be something to make sure players take free kicks etc. quickly anyway, both to keep matches flowing and to prevent an unfair disadvantage to the team creating the mini-break.