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It's got to be something more exotic than simply dumping energy into the target until it turns to vapor, otherwise there would be horrifying explosions of steam and guts and molten rock, instead of a soft hum and the disappearance of the target.
I choose to believe the vaporize function is actually a one way transporter beam. It digitizes them into the phaser and just deletes the file instead of sending it somewhere to be rebuilt.
That's a good theory! The development of one could have led to the other. A beam that remotely disassembles something to its subatomic particles without an explosion would have been a necessary part of transporter development, regardless of which was invented first.
Unless they operate on different physics than our universe currently does, there's no way around it. Energy is energy, it's the currency of the universe.
It's Star Trek. Of course it does.
In this case, it's a fictional particle doing the heavy lifting. Explanations of exactly what it's supposed to do seem to be inconsistent (it's Star Trek), but at lower energy levels, it does electromagnetic stuff (including stunning living creatures), at medium energy levels, it does thermal stuff, and at high energy levels, it messes with the strong nuclear force.
Disintegrating something by messing with the strong nuclear force would probably have harmful effects on anything nearby, which is not addressed because it's Star Trek.