The resupply priorities are hard to get right for all cases. At the moment, energy is balanced between ships as an absolute rather than relative quantity. When that ship reaches less than 550 energy, the tanker will start supplying it.
V has tried to get the priorities correct for ships with/without on-board generation, Guppies, ports of their own, combinations of ships inside/outside mine range, energy deficit, and varying numbers of tank modules. There is no one answer, and a manual-control system would take it from bad to worse.
Also, the game was built with the idea that a Varro would be unsustainably large. So 6000+ energy capacity is a fair distance from the designed size.