How to program Fio v3 without MicroUSB port
The board runs at 3.3V, so you can provide 3.3V directly into the 3.3V pin on the side. Also the black connector next to the USB socket is a battery connection for a Li-Ion battery or similar. It will take any voltage between 3.6V and 5V. Any higher and, according to the schematics, you need to remove the solder link that's just below the battery connector (silver blob). With that link removed you can theoretically go up to 20V on the battery input.

Yes, you can program through the 6-pin header below the main chip if you have a suitable hardware programmer (e.g., USBASP). That is a normal ICSP header like most Arduino boards have.