You'll need to use the barrel charger for applying firmware updates. The Lemur Pro has additional circuitry to support changing the battery even if it completely drained.
Just to be pedantic, USB-C does need negotiation before it provides 5V, but that negotiation is just a pair of resistors of a specific value.
(Since the USB-C cable is symmetric, this negotiation is necessary to decide which end will provide the power. One end has both resistors wired as a pull-down, and the other end has both resistors wired as a pull-up. The end with both resistors wired as a pull-up will initially provide the 5V power.)