What does this mean to the value of what we are "seeing"?
The example used before - that it is equivalent to a deaf man seeing a music visualisation - is apt. It is some sort of model, but not particularly close. It might still be useful, of course.
Not "seeing a music visualisation" (was it edited maybe?), reading braille. STM involves sticking a probe microscopically close to the thing-being-scanned, and reading how the surface's atoms deflect it. Which is very close to "literally feeling" the surface, as all "touch" is just electrons repelling each other at a distance - this is just at a slightly larger distance. https://en.wikipedia.org/wiki/Scanning_tunneling_microscope
Maybe a more human-scale-friendly analogy would be "finding the hot burner by moving your hand near it". In STM, each atom is a hot burner. You can pretty accurately figure out the arrangement of burners on your stove without needing to see or touch it.
What does this mean to the value of what we are "seeing"?
The example used before - that it is equivalent to a deaf man seeing a music visualisation - is apt. It is some sort of model, but not particularly close. It might still be useful, of course.