6.02 b) begins by saying while the pitcher is in the set position or in the windup. If this is not the case and there is a delay in the action, ie between pitches the batter may step out (in the comments part of 6.02 b). Also the batter is allowed to take time to receive signs from the coach. If the umpire chooses to ask the player to step in the box, then 6.02 c) may be applied.
The MLB differs from most other levels of play on this rule. In the MLB there is little to no concern over pace of play. It is rare to see an umpire warn a batter for taking his time between pitches.
One thing to consider about baseball is most calls are judgement calls. The rule book is vague. Things from the strike zone to what constitutes a delay are at the umpires discretion. The MLB ran into this earlier in 2014 with the "transfer" rule (2.0).
The are no penalties or fouls in baseball so it is often understood that umpires are seen as moderators instead of officials. If teams play slow, they play slow and vice verse for fast paced teams.
The Yankees and Red Sox are notorious for playing slow, and when they meet up games may exceed 4 hours.
In lower levels there is much more emphasis on this rule. Often at the high school levels and below, hitters are asked to keep one foot in the box while receiving signs from the coach. In college (NCAA) there is a time limit or pitch clock between innings and pitches.