I have a Moto X 2014, headphone jack also on the top.
1. No problem
2. Can't collide with charger cable
3. Good, when you have it in a charger station, it is still accessible.
Phones charge so quickly these days - they say the Pixel can get 7 hours usage on a 15 minute charge - that it begs the question, Why would anyone need a dedicated charger station?