The internal battery is in many ways superior to the external battery. I have both types on different bikes. While I have never had problems with the external battery getting damaged, the internal battery requires riders to be more vigilant about keeping it charged. That is, I own two external batteries and if for some reason one is low (or in one case dead) before a ride I can simply swap out batteries. This is not as easily done with the internal battery. One can even ride with an additional external battery in your pocket for added safety. So what do you do? Well if you get a Di2 D-Fly and a Garmin you can have the Garmin display the Di2 battery level on your screen as a percentage. This is what I have done for my internal battery mount.
On a more general note, I wish Shimano would stop listing the life of a full charge in distance. It is a pretty pointless metric. When I ride on flats I can go for thousands of miles without a recharge. On hills where I shift much, much more frequently (especially on the energy intensive front rings) I get about 400 miles. Also the batteries degrade with time like any rechargeable battery and so it gets harder and harder to judge the time/miles/shifts you have left before it goes dead. The little indicator lights in the front are very very rough measures. Frankly, Shimano needs to have the junction box display a percentage. Until then I would suggest getting a D-Fly.