IIRC, it is explained (kinda) that the personal viewpoint of being solid within the matter stream isn't entirely real. Wishywashy, but how do you show that on a screen, really?

To the bigger issue above, the function of the transporter is that the pattern buffer isn't "storage" such that you cannot query against the buffer as if it's data in memory where individual particles can be pinpointed. (Obv this is not necessarily canon and some episodes poke holes in the idea).

I've always imagined it more like a mound of dirt dumped onto a conveyor in FIFO order, sending it up the beam, then rolling in order into the pattern buffer. The buffer is just holding all the matter in a continuous conveyor in the original order so it can be reassembled on the pad. Outright saving a pattern to memory where every particle location, energy state, etc. would take basically all the memory everywhere (TNG: Lonely Among Us). Weapon and bacteria/virus patterns could be simple enough to detect within the buffer to knock those bits out as the "dirt" rolls around continuously.

And of course the longer you roll a bunch of dirt down a conveyor, the positions of particles shift out of their original position until eventually there's not enough of the original pattern to reassemble properly.

My headcanon for Scotty locking the buffer into a diagnostic loop means additional scrutiny in the system's pattern scanning which then keeps "knocking" bits back into place they were in the prior 'pass' down the conveyor in order to continue calibrating scanners.

Don't look at me like I'm crazy, it totally makes sense!!!!!!!!!¡!!!¡!!! *cough