The difference is the baseball clock has no reguard for radio broadcasts. The umpire doesn't always wait the entire 90 seconds between innings before asking for the hitter. In football, a guy stands out on the field and holds up the game until radio is ready.
I'm not involved with it in any way, but I have made the effort to notice when at the games to try to figure out why. I imagine it's a difficult situation to try to avoid. About all they can do is go to break as quickly as possible at the end of an inning instead of taking another 15-20 seconds to finish their thought.
The pitching change breaks for short mound visits are quite annoying, though. It's almost always at an important juncture in the game.