Regarding going by two different last names, it is very common out here (Southern California). As I mentioned in a previous post, I used to teach in Palm Springs (the general area Audrey and Jonathan went missing). I had two students who were sisters, one year apart. Their (not actual) names were Maria Garcia-Hernandez and Rosa Hernandez-Garcia. For whatever reason, their mother switched the order of the last names on the birth certificate. Sometimes the girls went by Hernandez and sometimes they went by Garcia. It only became an issue when their actual legal name was required. Oddly enough, I've had more than one set of siblings this situation has applied to. One set of siblings was not even Hispanic. It's just "a thing".
I have students who refuse to go by one of their last names because they do not like that side of the family. One student's name was Julita Romero-Fernandez. Fernandez, being the second name, it is what appeared on my roster. I would call roll, "Julita Fernandez," and she would ask me to not use that last name. I apologized, saying it's what was showing up and made an effort to call her by her preferred name, Julita Romero. I later found out she hated Fernandez because she'd been molested by someone in that family and other family members were also abusive. She did not want to be associated with them. (This has actually been the case with several of my students.) Another student hated one of her last names because it was her dad's last name and he abandoned the family.
I've had other students who just like to change their name from time-to-time, so they change which last name they use. And some students have one of the parents' last name as a middle name rather than part of a hyphenated last name and they want to use their middle name as their last name. None of this has even been an issue unless a legal document is involved. It's very common out here, in my experience.
Why Jonathan chose to do it, I cannot say, but for me it didn't seem odd. However, I can understand exactly why it jumped out to some of you.
As a side note, I had a student request that I call her Princess Moonshine of Aurora. I politely declined.