Does "one non-Logos card" on Phase Shift limit me, or just enable me?
It doesn't limit, it only enables. For every Phase Shift you play, you're going to be able to play one non-Logos card that turn. Here are some additional quotes from emails sent by Brad Andres (developer at FFG):


  The Wild Wormhole is creating it own play permission for
  the card it is playing from the top of the deck separate from the play
  permission that the Phase shift is creating. Meaning that you can
  still play a non-Logos card from playing the phase shift.


FFG also addressed this in this video.