The fare difference acts as a tie breaker between you and any other 35K flyers with the same credit-card status. Otherwise no effect.. EDIT: No effect "at the gate", but the more expensive "Flex PE" fare may give a 35K member opportunity for an upgrade more than 4-days in advance of the flight date. Unlikely, but possible.

EDIT: Error in the above. In the event that the eUpgrades go through, there's no extra fee if originally booked in PE-Flex. But PE-Lowest will then cost $200/passenger for the eUpgrade, in addition to the eUp credits. If the person applying for the eUps has SE status, then no fees regardless.