I always head-canon that the transporter pad auto adds .02mm to the Z-Axis of anything that beams in. Just far enough enough that a person won't really feel it, and objects don't rattle or tip from the tiny drop, but not too far so it's not as jarring. Of course a good transport operator can override this, to make an even "smoother" landing. If the tech can reassemble molecules, then why not have an accuracy of microns rather then millimeters? No chance of interphasing matter, if it never overlaps.
Not just your DNA, but the DNA of your micro biome, all your gut flora, everything you ate for lunch, the grease smeared on your face, and any alien infection you managed to bring up from the surface when you didn't wear protection
Okay, but like... Even if the decimal point is supposed to be two places over, how often is Starfleet replacing people's shoes after they get embedded in the deck plates by a millimeter? Do the floors of transporter rooms get permanently rubberized after enough use? Does Chief O'Brien have a special floor razor tool to scrape shoes off the pad when they're too deeply embedded to pull out?