Yes, I found
that first article a while back. Unfortunately, it does
not give a schematic and its description is confused.
As best I can figure it from the
version 0.9 schematic,
the "VUSB" is directly the 5 V Vcc pin of the USB connector. This connects through a diode - which
should be a Schottky but might not be - to the input of the 3 V regulator which is also the Vcc for the USB interface chip and "Vin". This means that feeding 5 V to "VUSB"
will (obviously) power the regulator - and thus the 3.3 V ESP chip - if connected to 5 V. You will lose a little in the diode, so taking power from "Vin" will see a lower voltage.
If on the other hand, you power it through "Vin", this will not feed back to "VUSB" and you might be able to feed more than 5 V - they say 7 to 12 -
except that the earlier schematic shows the USB interface chip fed from what is in fact "Vin" and this chip is not rated fro more than 6 V.
So I don't get that and I now recall going through this conundrum previously.

In any case, you power it through "Vin" and given the diode, there should be no problem connecting the USB connection for programming while it is powered through "Vin". The lack of a proper schematic does make this somewhat dodgy.