I like the way they "cure" him with antimatter and he
doesn't explode like a Warp Core breach!
Why would he?
He was exposed to a radiation treatment through anti-protons.
I fairly doubt that it would be hazardous to his health in a condition he was found if it's administered in low enough quantities.
Plus this is the 24th century we're talking about.
They have to be able to come up with a conversion process to extract what they need from usually dangerous sources in order to come up with potential solutions which can be used in other areas like medicine because space is unpredictable.
Also as I said before ... since Tom was occupying the entire universe at the same time, he could have possibly went through some area of it that triggered evolutionary process at an incredible rate.
SF only explored 11% of the galaxy, and we as a species have a limited understanding of the universe.
Who knows how would individual areas of the universe affect us in reality ... let alone in Star Trek.
Although ... the episode WAS kicked out of canon.
The later season ('Day of Honor' episode) confirms that by Torres stating: 'We don't know anything about TW technology. Playing around with it could be dangerous.'
And Tom stating something along the lines of not flying through TW before (in the same episode).
So technically speaking the episode happened yes. However, is it part of canon? Unfortunately no.
I'd personally want it to be, but alas, it's been kicked out of canon and it stuck like that in later seasons.
Honestly, why can't the writers come up with decent explanations for some of the episodes that apparently made 'no sense'?
I mean come on ... when speaking on a universal scale, MANY things won't make sense.
Heck we have things in real-life that make scientists question themselves and the established laws of physics by examining phenomena in our solar system alone and outside of it (through a telescope no less).