I think you just inadvertently solved the question of what happened to transwarp drive: It could be that the tech did not have to fail, but when a "regular" warp core was tried out in the same space during testing, the added cooling from the "fins" in the neck, nacelles and "bulge" made warp drive just as effective in getting certain speeds.
The Ambassador and Galaxy have limited fins in the neck, but they still have fins in their nacelles, as do most other newer ships. That would also explain why Voyager was able to have Paris break the barrier so easily, it was not the tech that needed developed from scratch, but adapting it to a shuttle and tying to get even more speed out of it to approach warp 10.
I think that the version of the ship with two deflection crystals should have two cores, because otherwise there would need to be a system at the "split point" where the energy is sent to one crystal or the other
(This is unlike the Constellation-class which has two crystals at different ends of the impulse section. In that case I think the warp core is mounted transversely, going from one crystal to the other. I had some way of explaining the vertical core section in the Hathaway, that is not important now.)
Why couldn't this scene be on the Excelsior and the monitor was showing the status of the allied ship (NCC-1701-A)? The warp core placard in the hall could be what is showing Excelsior's status, and it would not need to be on two monitors at once.
A problem in continuity is exactly what that placard shows. It was made for Leah Brahm's lab. Leah refers to it as the "engine" she designed. We know that some of the Wolf-359 ships had TNG-style nacelles, but lower numbers, implying older ships, so Leah must have designed the TNG warp core, not the TNG nacelles. That means that showing that core on NCC-1701-A or NCC-2000 appears to be a problem with timing. The only solution I can think of is that the external appearance of the core in the 2290's is the same, but Dr. Brahms developed or changed something about the internal reaction chamber. Otherwise, it would not make sense to have this core, and especial not this placard, on either ship in ST:6.