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 However, its a bit outdated as "SLOTS" are 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).
 

On Tuesday, July 2, 2019 at 11:17:22 AM UTC-4, TJF wrote:
>
> Am Dienstag, 2. Juli 2019 16:28:04 UTC+2 schrieb LuminousShadow:
>>
>> You can have the pins configured upon bootup with a custom device tree 
>> overlay.
>>
>
> Yes, you can specify the mux mode to connect the pin to the output of the 
> eCAP module in a device tree blob. But can you configure the modules 
> registers to generate a certain output?
>
> I'd try a start script for systemd, ie. invoking a small libpruio prg to 
> enable the desired output.
>
> Regards
>

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