Workout Builder structured workouts enable you to export your workouts to your training devices. The bike workouts are created by me (Phil Mosley) based on a % of your Functional Threshold Power. Whereas the run workouts are based on a % of your Threshold Run Pace.
There is no easy way to change this to Heart Rate at the moment, aside from re-creating the structured workout in Training Peaks based on the Description, using heart rate. Hopefully Training Peaks will make this possible soon.
You can still train effectively by using the Workout Description and your training zones based on heart rate or RPE, although you cannot export the workouts to heartrate-only devices.
It is actually very hard to follow structured workouts on your watch based on heart rate alone. This is because the heart can take several minutes to fully reflect how hard you’re riding or running.
For example, on the bike your power output might go from 200 to 400 watts in one second. But your heart rate would not reflect this doubling of power output, unless you sustained that 400 watts for at least 30 seconds (probably more).
Heart rate monitoring is great for steady state rides or long steady runs. For the shorter interval sessions it is better to go by RPE (or ideally power or pace) and then use heart rate as a back up measure of intensity.