There's no confusion and they ARE brand exclusive. It's not like they'll be showing up to each other's shows. One is on Raw the other is on Smackdown. Asuka's title is a continuation of the Raw Women's Championship's lineage which was originally the WWE Women's Championship anyway, Rhea's title continues the Smackdown Women's Championship's lineage that's it. The only difference is now the lineage of the title doesn't have to be severed every time they decide to switch the Champions. Charlotte got like 2 free "reigns" just off that, it's nonsense.
Absolutely nothing has actually changed for the viewer the only difference is they're not hamstrung by the name of the belts so they don't have to worry about booking themselves into a corner with a dominant champion who has pretty much exhausted all of their challengers on a show (I.e. Bianca) they can just switch brands and have that person maintain that run whilst having a new cast of people to work with, no different to what Gunther is doing with the IC belt.
I guarantee in less than two years, they're going to do title vs title and unify the women's belts. This is just a temporary solution until they figure out how they want to do it.
Also, there's nothing that says that champions have to switch shows. If they run into a Bianca problem, they can have that champion lose (like they did with Bianca, making it pointless that she was drafted in the first place) or draft wrestlers from the other brand. From September 2016 to November 2018, A.J. was WWE Champion for most of that time and he never left SmackDown. They just gave him different people to feud with.
Or they could have just went back in time to 2016, realized calling a title after its brand wasn't going to work long-term, and just did what they're doing now. The Universal Championship was designed for RAW, but when it went to SmackDown, all they had to do was give it a different color. There were ways around this, and they're things that I've seen them do for as long as I've been a fan.