[beagleboard] DTO pinmux settings are not applying

My questions are this: Is there anything else that needs to be added to
this DTO to get the new pin mux settings applied correctly for these four
pins?

I can't make sense of what you're doing, so I don't know.

Am I missing in the SRM documentation somewhere these pins can't be muxed
to something different?

All the pins except for some special purpose ones (like DRAM and analog
inputs) can be muxed.

Apologies if something doesn't make sense in my post... I'm still quite a
newbie to device tree overlays.

Almost nothing made any sense, and what bits did make sense seemed
contradicted by other things you mentioned. Be as specific and exact as
possible in your questions, include what you tried, what you expected to
happen, what _actually_ happened, and someone might be able to help you.
Also, obfuscating your situation by "helpfully" chopping out huge
chunks of your configuration files isn't a good way to get help. If
your files are too big for an email, post a link to them on github,
dropbox, Google drive, or wherever.