FWIW, Zeke has always left the game for a breather. In his first two seasons, we used to pull him during our 3rd drive (which would usually come around the beginning of the second quarter) and put in the backup. Zeke would pretty much take every snap from there on out. This last year, it looks like we gave Zeke more freedom to leave the game whenever he gassed out.
The total number of reps really hasn't changed, it's just more visible to fans when 21's jogging to the sidelines, and they didn't really notice when he wasn't coming on the field for a drive at all.