My one issue with that line in the episode Day of the Dove" -The Star Trek transporter technology itself is able to disassemble and put back together the atoms of a human being (of which there are billions) nearly instantaneously.
The technology can do all that; yet Spock is claiming, that it effectively can't beam a person to an exact point on the ground or in a ship?
Seriously?
My point is this: every time they're shown beaming down or beaming up they are placed exactly on the ground. If the transporter put them even a micron beneath the ground they're beaming onto, It would cause serious injury, or possibly death. For it to work as it does it would have to be incredibly accurate 100% of the time, no matter where you're beaming to, or it wouldn't be safe for anyone or anything to use.
Ergo, intra-ship beaming should be no more dangerous than beaming down to an uneven planet surface.