On my EB48 2.0, I have opted to cut those wire guides off the side rail, it was a PITA to re-route the wiring when doing rebuilds, I had accidentally got the servo wire tucked under the servo tray which pinched the wire and made a clean cut. I've since used double-sided tape in the channel slot behind the servo to prevent the wire from sliding out of place and no more fuss with routing the wiring along the rail.

As far as using the USB dongle goes, I completely remove the servo from the car to program it once and that's it, not really sure what needs to be programmed on the servo after it's installed in the car, at least for what I need out of the servo where the only 2 settings that I've changed from default are maxing out the PWM Power and enabling "Soft Start".

I was tempted to increase the servo angle, but my EPA is already at 94% with the steering stops removed so don't really need to add any more throw as it is.