It's important to recognise that the episode that you're referring to is about as close as a TV episode can get to becoming "non-canon". As well as being recognised as the single worst episode of Voyager (and frequently voted the "worst of trek"), even the writers accept that there were many technical failings with the description of how Transwarp works in the episode.

Brannon Braga describes it thusly;

"It's a terrible episode. People are very unforgiving about that episode. I've written well over a hundred episodes of Star Trek, yet it seems to be the only episode anyone brings up, you know? 'Brannon Braga, who wrote 'Threshold'!' Out of a hundred and some episodes, you're gonna have some stinkers! Unfortunately, that was a royal, steaming stinker."

Rick Sternbach tried to handwave the whole episode away;

""I think what may have happened with the silly Warp 10 episode was that there was a coupling of the energy from the shuttle to all of the energy and matter of the universe (which might be possible if we're looking at a finite system), and the shuttle was able to access any point anywhere by some amazing tunnelling phenomenon which shrank the normal 3D distances to points, much like all the universe being squished into a pinpoint at the big bang because it was all energy with no need for elbow room. Whew."

It's important to recognise that the episode that you're referring to is about as close as a TV episode can get to becoming "non-canon". As well as being recognised as the single worst episode of Voyager (and frequently voted the "worst of trek"), even the writers accept that there were many technical failings with the description of how Transwarp works in the episode.

TNG's Producer Brannon Braga describes it thusly;

"It's a terrible episode. People are very unforgiving about that episode. I've written well over a hundred episodes of Star Trek, yet it seems to be the only episode anyone brings up, you know? 'Brannon Braga, who wrote 'Threshold'!' Out of a hundred and some episodes, you're gonna have some stinkers! Unfortunately, that was a royal, steaming stinker."

and TNG's 'Senior Technical Consultant' Rick Sternbach basically tried to handwave the whole episode away;

""I think what may have happened with the silly Warp 10 episode was that there was a coupling of the energy from the shuttle to all of the energy and matter of the universe (which might be possible if we're looking at a finite system), and the shuttle was able to access any point anywhere by some amazing tunnelling phenomenon which shrank the normal 3D distances to points, much like all the universe being squished into a pinpoint at the big bang because it was all energy with no need for elbow room. Whew."