Why would it confuse the casual viewer? The old trek is still out there and so are the spin off series the last one which ended only 10 years ago. Unless new fans are only 10 I think most know about the prime universe. I would guess that new fans in their teens or 20s so they surely know what Prime Trek is and anyone older who never watched trek know about the old show anyway.
I disagree. The new Trek films have also been an opportunity for me to see just how little my friends know about Prime Trek. I asked everyone in my group of friends who are aged from mid 20's right up to 40 whether or not they got the reverse reactor scene in STID and not one of them knew what I was talking about, they just enjoyed the film for what it was. A couple of them even said that 'old Star Trek is shit' when they probably barely watched it.
My seventy year old parents didn't remember they'd even seen TWOK when they watched STID and didn't make the connection, despite watching it with us as a family when we were younger.
People like us who have seen most or all of Prime Trek are in a minority of people in my opinion.
Having to explain to people like this that we're back in the Prime Timeline and not the new one during a film for example would probably be clunky, hurt the plot and confuse new viewers. It worked for the reboot as it was kept simple, and to a couple of lines of dialogue, but how would you explain that you're going back to another universe whilst making clear it's the universe of an older group of films and TV shows that the viewer is barely aware of?