If transporters really work the way Star Trek claims there is absolutely no reason they would constantly get blocked by magnesite, random stones, atmospheric interference, or whatever the current MacGuffin of the week is.

Perhaps the things you mention really only interfere with the transporters sensor’s in some way

Skimming memory alpha Magnesite does interfere with sensor and transporter functions but memory alpha doesn’t specify if the transporter function interference is related to the transporter sensors or not

I don’t see how random stones apply here as it could be any kind of stone and you’d have to be more specific, transporters can already discern rocks from people, i think i recall hearing something about subspace shadows somewhere but i cannot recall where i heard it so i cant confirm subspace shadows