In that episode Tom Paris reaches warp ten in the delta flyer only on the holodeck.
Yes, but "Threshold" made it explicit in dialogue that "reaching warp 10" meant achieving infinite velocity:
http://www.chakoteya.net/Voyager/212.htm
KIM: Nothing in the universe can go warp ten. It's a theoretical impossibility. In principle, if you were ever to reach warp ten, you'd be travelling at infinite velocity.
NEELIX: Infinite velocity. Got it. So that means very fast.
PARIS: It means that you would occupy every point in the universe simultaneously. In theory, you could go any place in the wink of an eye. Time and distance would have no meaning.
(This is because travel time is distance divided by velocity, so as velocity goes to infinity, travel time goes to zero, which is equivalent to occupying both starting point and destination at the same time. But
any nonzero number divided by infinity is zero, thus at infinite velocity it takes zero time to cover any and all distances, therefore you occupy
every point at the same time.)
See, this is why it was dumb to call infinite speed "warp 10." Applying a finite number to infinity just confuses people because they don't understand it's meant to be infinite.
Also, the problem with the idea of "reaching warp 10" is that you can't reach infinity, by definition. The word "infinite" is Latin for "unending." It's not a destination, it's a direction, something you endlessly head toward and never get any closer to. If you accelerated at warp for a hundred trillion years, you'd be exactly as far from infinite speed as you were when you started, because infinity is not reachable, ever. There is no point on a graph you can ever label "∞" -- just an arrow pointing in that direction. After all, if infinity were a point, you could go beyond it, and it wouldn't be infinity.
So the very premise of "Threshold" -- that Warp 10 is an actual reachable velocity -- doesn't make physical or practical sense. The only way I could ever rationalize it in my head was that the shuttle didn't actually accelerate to infinite speed in the "normal" warp-acceleration way, since that would've taken an infinite amount of time. Instead, the "transwarp threshold" that the characters talked about had to be some kind of quantum leap, an instantaneous transition from a finite velocity state to an infinite one. But then, that's not actually a speed at all, it's just nonlocality, becoming an entity that occupies the entire universe simultaneously.
I always figured that the nonlocal "transwarp state" they entered must've been the Q Continuum or something connected to it, and that the whole "salamander evolution" thing was just some Q-induced effect to scare mere mortals off of dabbling in the Q's domain.
But then the writers themselves essentially declared the episode non-canonical, so I just ignore it these days. Although I've considered the possibility that the first test flight actually failed and everything after it was just a dream/hallucination Tom had before the Doctor brought him out of it offscreen.