Ports

You can use any of the ports to charge.

I am sure the speed will be limited by your card or the reader, so while I would say the USB-C port would be best (save the TB ports for TB!), it probably does not matter.

It isn't really an issue, however many users are finding it is easier if they have a Thunderbolt dock to connect their legacy devices. One I'd recommend is the OWC Thunderbolt Docks, Docking Stations, and More (macsales.com)

When you decide which to use given with the external devices you decided to purchase before. An example would be buy a USB flash drive and use it on the USB port. Buy an OWC thunderbolt external and insert your own NVMe SSD and use it on the thunderbolt port. It can go on for as much money you want to spend on the devices.

When I plugged my TB2->TB3 adapter into the USB-C port, I got a warning that it had to be plugged into a TB port, so there is a difference. I would suggest plugging known TB devices into the TB ports and known USB-C devices into the USB-C ports.