I have this same problem with a polar heart rate monitor. rideWithGPS shows the current heart rate, and the exported data from mission control shows it as well, and it matches, but while riding, mission control doesn't display it. I actually assumed it wasn't even reading it until I noticed that it was in the output file.
I export the mission control data to strava, and it's very complete and clean, but before I had the polar strap I would use the apple watch with rideWithGPS and merge the two data files with gotoes.org, which is very easy and fast. you just upload the two files, pick which streams you want (i'd only grab heart rate from the rwGPS data) and then it makes a new one.