If the procedure is FDA approved than I would see no reason why you could not use this methodology. There is a list of approved standards on the FDA Web site.  If this is not on the site, then you may need to perform an internal validation showing it is better to support your cause for using this test method.

Positive migration would be the forcing out of atmosphere inside of a package by internally pressurizing the package (blowing it up like a balloon). The negative migration would also be the forcing out of atmosphere from the package, but it is done by changing the atmosphere outside of the package (vacuum test simulating an airplane environment when pressurization is lost). This could potentially draw in the outside atmosphere at equilibrium.

A more simple explanation might be that positive migration pushes out atmosphere while negative migration draws in atmosphere.