BACKGROUND: Heart rate does not quantify the actual load. It quantifies the total stress on the individual. The longer the work period, the more closely heart rate quantifies the load. The shorter the work period, the less it quantifies the load.
So for EMOM training, although your heart rate monitor may say that you’re in Zone 2 the whole time, I suspect very little of the workout was in Zone 2. You were either way above, or way below, and the average of the work/rest periods creates a stress load equivalent to what an extended period in Zone 2 would be like.
Same level of stress on the body. Very different levels of stress on the muscles.
In other words, 45′ of EMOM in the gym will not help your running as much as 45′ on the trail. Or vice versa. I don’t think there’s any harm to it, as long as you think of the two activities as distinct.
Does that make sense?