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I'm asking as everyone in tutorials apply it onto the mesh but they don't explain it properly.
It seems to me that it causes some problems. But I still didn't get why it causes problems if I don't apply location, rotation, scale to a mesh.
It's not only physics but most of all modifiers that require it. When you don't apply Loc, Rot, Scale the modifs give undesired effects in the way they remember previous state. Try it!