From the opinion of the court, "If the test could be satisfied merely by the fact that an employer required an activity, it would sweep into 'principal activities' the very activities that the Portal-to-Portal Act was designed to address".

The Portal-to-Portal Act was in response to miners suing for back pay the time they spent moving between mines (after Congress enacted laws that made that seem like a winnable case). It was understood and customary that the time was to be unpaid (thus presumably their wages already took that into account).

The relevant portions of the Portal-to-Portal Act (as quoted by the court) are:

  (a) Except as provided in subsection (b) [which covers work compensable by
      contract or custom], no employer shall be subject to any liability or
      punishment under the Fair Labor Standards Act of 1938, as amended, ... on
      account of the failure of such employer ... to pay an employee overtime
      compensation, for or on account of any of the following activities of such
      employee engaged in on or after the date of the enactment of this Act— 
	(1) walking, riding, or traveling to and from the actual place of
            performance of the principal activity or activities which such
            employee is employed to perform, and
	(2) activities which are preliminary to or postliminary to said
            principal activity or activities, “which occur either prior to the
            time on any particular workday at which such employee commences, or
            subsequent to the time on any particular workday at which he ceases,
            such principal activity or activities.

So there's an exception for activities which are customarily paid. I am not sure why the court worried that paying these temp workers would go against what the Act was designed to address. Most people would expect a required security screening like this one would be customarily paid time, thus is has to be paid under the law.