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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.
The lesser known Venn diagram with no overlapping center.
I mean it's precise enough to assemble your DNA atom by atom, I think it can put your feet directly onto the floor?
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
not my feet they smell