I'd be tempted to run them through the rear plastics, and then under the seat.
The only thing needed from the SCv2 charging array is access to is the AUX charging port. No need to route through the internals of the bike.
While this install looks very clean and well-thought-out, the best result will always involve minimizing chafing, bending, and movement of the cables. Routing the cables under the seat with some mesh sheathing seems like a good idea aside from the bend needed to get there from that port.
Of course, I'm more comfortable attaching the cables to the controller's battery terminals, partly because I know that when I place that end of the cabling, it won't move.
I think for running the cables outside, a stiff shrink-wrap tube and a mesh sheath around the cables might help, tucked just under the edge of the seat and probably zip-tied to the top rack bars.
I should warn that leaving a cable like this plugged into the accessory charging port makes the bike vulnerable to cutouts from moisture on the signal pins in the accessory inlet, particularly in a heavy rain. I've had a bike cut out on me because I left a Y-splitter plugged into the port and it even got the fault while the rubber boots covered both Y plugs. Again, in a heavy rain.
dukecola does seem to have some of these risks in mind, but it's worth mentioning.