Fanfic ideas

[Custos Sophiae]

I think part of the issue is one that's more of an externally imposed cultural difference.
Which explains the B5 end, but not the Trek end. Why has no-one in Trek heard of jump gates, or hyperspace? Even if they added nothing to Trek tech capabilities, debatable, it's still the kind of discovery that would win a Noble prize. Someone would have to be supressing it, in every one of a myriad worlds, and if that, what else?
The implications could cast the entire Trek universe in a different light. How much of what Q, the Organians, and their like have said and implied is true, how much part of some vast experiment? Could the great barrier round the galaxy just be the wall of a petri dish? And so on.
(I could ask too about Jack the Ripper, in one universe a man recruited by the Vorlons, in the other an energy being, and yet they did the exact same thing. That's too big a coincidence not be planned, but by who?)
You may not want to open those bags of worms..
Makes you wonder if the Organians and Melkots and Q are playing their own game against the Shadows and Vorlons, in A Thin Veneer, doesn't it?
There are names for those who use force to impose their views on those too weak to fight back, some good, some bad; but they apply just as much to godlike powers acting through unwitting proxies. Both Shadows and Vorlons are certainly wrong, but Q doesn't strike me as an embodiment of right either. He's a trickster, never to be trusted.
However, all this is really answering the wrong question.
What really matters is not how the Trek and B5 universe work, but what makes a good story?
The story comes first, always.
When the scenery comes first, you have a travelogue. When the author's philosophy come first, you have propaganda. (Plot and character I'm counting as two halves of a whole; a great story needs both, working well together.)
Both canons are loosely enough defined that an author can easily bend them to fit almost any story, a simple matter of flexible interpretation. With a good author, and a good story, the reader will neither notice nor care.
If the Enterprise crew vastly outgun their antagonists they can easily come across as smug bullies, a trap which takes a skilled author to avoid. Inventing a small incompatability in the laws of physics (and it would be pure authorial invention) is just one way of levelling the playing field, and avoiding that problem, for the sake of a better story.

[Custos Sophiae]

That's some input! Especially about the Cthulu Mythos
A useful thing about the Cthulhu mythos is its flexible membership. You can easily add many villains from other sources to its ranks.
Rowley's Vang Omniform would work quite well as one of its lesser menaces. They're a intelligent superparasite, with tentacles, and polyps. Their original empire was destroyed when their enemies blew up all their home stars, but the Vang survived, though forced into deep hibernation until prey should come within reach. (In one scene, cybernetic soldiers are exploring the wrong derelict when vines come out of the ceiling, yank them off their feet, and burn through their armour to devour their living brains.) They will disguise themselves as human when necessary, but when that phase is past they warp their hosts into horrendous shapes, growing new organ, many of them unpleasantly visible.
The Fendahl, from Doctor Who, would be a mid level menace. What the Doctor fought was a crippled ghost, a fossilised memory stirred to unlife after 12 million years, yet it could have devoured all life on the Earth within a year, and the sight of it killed.
The Fendahl-eater, product of one of the Time Lords' more ill-advised weapons projects, would rank near the elder gods themselves. It was not made from matter or energy, which the Fendahl could have devoured; it was a form of malefic space which, once released from its prison, could have devoured all space and time, from here to the furthest star, from the big bang to the last trump, all in a subjective hour. Afterwards, nothing would ever have existed, or ever exist, except an all-devouring void.
And there are more where they came from, many more. With the Cthulhu mythos, you can pick from among the horrors conjured up by a century of SF writers, and they have no lack of imagination.
Pitting Kirk against all the armies of nightmare might be overkill, and depicting a convincing yet meaningful win would be challenging, but a dozen mythos-compatable villain races, some only appearing off-stage, could be quite effective

[ECSNorway]

Which explains the B5 end, but not the Trek end. Why has no-one in Trek heard of jump gates, or hyperspace? Even if they added nothing to Trek tech capabilities, debatable, it's still the kind of discovery that would win a Noble prize. Someone would have to be supressing it, in every one of a myriad worlds, and if that, what else?
An interesting point of B5 continuity, that.
It's mentioned in certain parts of the source material that B5 jump drive is actually a form of interdimensional physics that normally takes younger races tens of thousands of years to develop. One race of the Ancients, the Kirishiac, actually had an interstellar empire founded on STL ships before they ran into the Vorlons and fought a major war against both them and the Shadows... and unlike Johnny Nuke'em, had weapon and defense technology nearly on a par with them.
This lead to the Vorlons' initial creation of the jump-gate network, which they made deliberately possible for the younger races to reverse-engineer and use for themselves. Specifically in order to make sure that people engaged in empire-building and such get -noticed- by the Gameplayers.--
"Use of unnecessary violence in the apprehension of General Zod has been approved."
--
Sucrose Octanitrate.
Proof positive that with sufficient motivation, you can make anything explode.

[Custos Sophiae]

It's mentioned in certain parts of the source material that B5 jump drive is actually a form of interdimensional physics that normally takes younger races tens of thousands of years to develop
Interesting, I hadn't come across that before.
You will have realised, of course, that this is evidence in favour of incompatible physical laws. If the Kirishiac, with technology on a near par with the Vorlons, didn't develop a warp drive, despite the absence of Vorlon/Shadow intervention, that suggests that, at the very least a B5 warp drive would require Vorlon level tech, as would any comparable none-jump FTL drive.
In the opposite direction, if you consider the Trek reset button, all those technologies used once and never again, even when reuse would seem appropriate, it's a pattern entirely consistent with Trek tech being suppressed. It may advance a little over the various series, but compared to a reasonable extrapolation, it is practically stagnant.
Neither argument is irrefutable proof though. That is a chimera. There can be no proof, and (as this discussion demonstrates) any attempt at one would be futile. Both canons are amenable to flexible interpretation, within broad limits (broader for a crossover), which leaves the fanfic author free to choose whichever interpretation makes for the best story.
Other canons, such as Middle-Earth, are more tightly constructed, leaving less leeway for the author, but they are most the work of lone authors, not a stable of writers, even with guidelines.
Anyway, I'll look forward to seeing what approach A117 takes.