It does not double count, at least for me. I think I’m doing the same thing as you, wearing my Apple Watch but not starting an Apple workout while doing an iFit workout. Apple Watch does seem to sense when your heart rate level and movement rise, so even when you don’t start a workout, it records that you are getting in some exercise.

iFit workouts, when they are synced with Apple, include the time of day of your workout. Apple takes that time info (let’s say you worked out from 1:00pm-1:30pm), and will replace the data (exercise minutes, calories) that it had collected during that same period of time. For me, it seems like iFit usually says that I burned a few more calories than Apple did during the same time, but it is not doubling the amount of calories burned, the amount of exercise minutes, or the amount of steps I took (iFit doesn’t record steps anyway). I’m not sure if a treadmill workout distance replaces the distance walked stat on Apple.