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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.

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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!

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    $\begingroup$ This answer is kind of misleading, since apply location and all other stuff basically mean changing the data inside mesh object container. Those data will been used by most of the modifiers. There is no previous state in modifiers apply process. $\endgroup$ – HikariTW Jul 26 '20 at 9:39

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