Although I have no experience with the WiFi version;
I'll agree with you the documentation could be improved with this bit of detail. Do you currently have the WiFI board, or are you considering a purchase?
Have you checked out these resources:
Note the section in red, just below 'Pins not on connectors'
So, it appears that 3.3v could be supplied to pin J2-3 , Gnd to J2-1 , rather than and instead of powering via the micro USB
See EDIT below
This would mean of course, tack soldering your JST connector choice to the top of the header pins.
Note: The schematic shows both VBUS and VUSB All text documents refer to VUSB Not sure if this was intentional, or just to differentiate between power in via the connector VBUS and that used to supply circuits on the board itself VUSB.
This detail should suffice in the meantime until another with actual hands-on experience can assist here.
From the bullet list just below 'Pinout'
"3.3 is a 3.3v output from the on-board Voltage regulator."
Although this pin is on the downside of the regulator, there isn't any reason schematically this couldn't be used as a supply pin. However, just now locating this comment, leaves me with a bit of doubt, as it is specified as an output pin. So, not sure if my suggestion to tack solder a connector here is prudent.
Maybe, J2-2 labeled VBUS (on schematic VUSB on diagram) could be used as long as the battery supply is above the voltage regulator input requirement.
"On-board 3.3v 250mA voltage regulator, accepts voltages from 3.5v to 5v"