Being after voyageur wont work.
Holo technology, borg technology, post dominion war, opens a can of worms of technology.
Magic was essentially introduced to the series
An airplane would have seemed like magic to humans for most of our history. The human condition in the context of advancing technology is a core interest of science fiction. What would it mean to be human in a world where genetic manipulation allows humanity 2.0? With advanced AI, clones, self aware androids, nanotechnology, virtual reality, etc. This is SciFi. I would run with the technology and explore the changes it would bring, and how our protagonists and antagonists negotiate this world.
With 2391, what seems to be the issue? Even if every Starfleet ship in 2391 has been retrofitted with Future Janeways "transphasic" torpedoes, so what? Other than being more powerful than photon torpedoes, what really changes? The weaponry of Starfleet would advance anyway, so whats the issue. The Enterprise C (nevermind the D or E) would probably overwhelm Kirk's Enterprise with ease. Yes, I am sure info from 7 of 9, future Janeway, the Voyager database, and research from the Dominion War are all shaping the Federation of 2391. But great stories can still be told. It's not like you have lost anything.
I wouldnt worry about disrupting the JJverse. It's a different universe, so the Prime events will not be an issue.