I’ve always been suspicious of any explanation they gave for their molecule scrambler. Starfleet is at core a military establishment, and they will say any kind of lie to keep the plebs in line and everything running smoothly. Also, I think the buffer allows them to use some sort of mass reserve to fix missing bits, I think Scotty explained something like that when he put himself in the buffer and turned on the refresh to cycle, and it just did the whole thing for Riker. Now, whether that buffer is holding particles or just a record of the poor destroyed original, I don’t know what to believe. (All speculation of course, based on years of transporter incidents.)