You can have the pins configured upon bootup with a custom device tree overlay.
Yes you can. By creating the device tree binary overlay you can not only set the mux mode, but its output as well.I'll add another resource that explains this:http://derekmolloy.ie/gpios-on-the-beaglebone-black-using-device-tree-overlays/ (basically a walk-through on how to do it. However, its a bit outdated as "SLOTS" are obsolete).