The user/D1 you refer to had a little bit of rust however that wasn't the issue - the issue was the pins were seized from electrolysis. It's exactly how we say the port shouldn't be installed - if the injection moulded lead from your phone is at the bottom then water can't drain and creates a bath for which the 5V between the pins to pass. Two days is all it took for it to fail.
Is it an issue? Absolutely, but you'll have the same problem with any USB device not just the D1 - which is why our port is outside the device. Better to replace the port then throwing it in the trash sometime after the 1yr warranty ends (that's not the D1 warranty).
Ideally cable tie the connector directly under the stem with the wires from both the D1 and the USB device cable bending a little towards the ground - that way water can't hit it from above and water can't run into it.
The problem with waterproofing is once it fails the water sits there and creates this bath of water in which the pins dissolve. We made the port drainable (not via injection moulding which is half the price) to prevent this (it's not perfect but it's something) - but the user must have the D1 port at the bottom. It's not perfect though, any path the electricity can take between the 5v and 0v of the USB port will eat the pins.
I highly recommend installing under the stem for a long life. A dab of WD40/GT80 may help as well. If it does fail, we have the service on the website to replace it. Cost is about £5 posted back to you.
We're looking for alternatives but haven't found one as of yet. Prevention is better than cure - there are D1's touring the world for over 6 months now, no problems. It's all about how you install the port as to how long it'll last.
The D1 main unit should last forever. Zero failures so far, a record we are mighty proud off.