The advantages of having charging port on top? [not relevant]

If you want to use your phone while charging it's more convenient to have the charging port on top otherwise you have to bend the cable beneath the phone in an odd way.

@Xiph I would say exactly the opposite. If the charger port is on the bottom, you can hold the phone like it was the receiver of an ancient analog telephone. Comparing the Jolla to (example) the Samsung Galaxy S3 the location of the port is much better with the S3.

Usually power plugs are lower than your ear. In Finland usually close to the floors and sometimes at waist height :) That said the cable comes from a lower point and has to bend before going into the phone. The extra bending will take maybe 20cm of cable length.

My idea is to engineer together an other half that offers a bottom micro usb connector and a flat wiring attached to the TOH that matches the power pins available fron Jolla (next to the SIM card slot if I remember correctly). It may be considered also whether the top USB port should be hidden by the TOH

I'm not an expert but my best guess is it might have something to do with the circuit design to make the phone smaller/make everything fit nicely? The phone itself is quite thin and you don't have all the space in the world to place and wire every component where you originally want.