All models have preset texture paths(and not all are NameOfTexture.blp with no path). Changing those is in no way disallowed, as it's considered a minor edit and doesn't really affect the model's use or appearance at all.
Also, you can't just put the BLPs anywhere in the MPQ. The texture paths must still be obeyed.
Thus, there's no real gain from placing them in an MPQ. Only extra problems, such as the chance to mess up your MPQ and the need to use a separate program just for this.
Furthermore, MPQ edits are harder to copy over, making them less user-friendly, unless you make an executable for this very purpose, which in turn also requires skills and provides new ways to mess up.
A folder can simply be unzipped into the right place and it works.
So basically, why spend more effort and get a worse result?
For all practical purposes, using folder(s) is better.