Your current method works for me. I like seeing cross-over characters pop in. This is mainly because it serves as a kind of quick fix for my desire to read about other characters. That doesn't mean there aren't dangers inherent to that approach. It's difficult for me to step outside of my experience and pretend that I don't know who you are talking about when characters from nonlocal realities pop in, so it's hard for me to tell if things get unwieldy for new readers. I know you've worked to make that a non-issue, but it's invisible to me, which is probably the plan.
I can tell you that I would be just as happy if the universes are kept separate if that is the difference between more books and no books. Consider that if the primary point of friction with your readers is the multiverse that you don't actually have to contend with that. Your worlds are rich enough to explore stories without recourse to the larger conflict and still feel fulfilling. Additionally, you can always start new worlds with interesting characters. It's difficult to know whether that would solve your problem because, given what you've told us, the other half the of the problem is deliberate rather than simple reactions to story structure.