tests: bluetooth gatt settings: Fix random test failures

These tests are creating and deleting temporary files.
But they deleted them with a wildcard that
matched each other's temporary files causing failures
when the tests run in parallel.
Avoid it by only deleting the files for each test.

As a freeby: Add the option to pass arbitrary commands to Phy from the
calling script, as with most other tests

Signed-off-by: Alberto Escolar Piedras <alberto.escolar.piedras@nordicsemi.no>