It's not too much of a problem. For the month or so I used both, I'd use the reader for the regular scans every 20 or 30 minutes (well, why not, some people chew pens, I scan), and then just scan the app every eight hours or so (when you scan, it'll then ping you a message eight hours later as a reminder if you haven't scanned between times). That way, even if you're not using the app for regular scans, you'll still get the full graph for the last eight hours.
I'll give the app it's due: graphs on the reader can look a bit 'stabby' because the screen size is so titchy, and can make a day look like a mess, whereas the app is running on a wider phone screen, so the same period looks smoother and, I think, is closer to the reality of it.
Still, I decided not to use it. The noise is a couple of bleeps, but I'd still have people in the office saying, oh, is that you bleeping again. They didn't mean any harm by it, just joshing and I've known them long enough to let them off with it, but it's nobody's business if I decide to scan.
There's apparently an app which kills the beep but couldn't be bothered with it.
Also, there was one occasion when I was in a pub, decided to use the app, lit screen is facing out into the body of the crowd, was having trouble finding the sensor with it (had only had one pint, honest!), and I swear I was getting the evil eye from this guy who seemed to think I was filming his girlfriend with it!
So, sure, the idea of casually waving your phone past your arm seems kinda funky, but in practice, maybe not so much!