I would think you would use the greater of the elected flat dollar amount or the auto-escalated percentage, computed each pay period. For example, it's the participant's 2nd year so their auto-escalation rate is 5%. When they first became eligible, they elected to contribute $50 per paycheck and have not made an affirmative election for the second year. Week 1, their pay is $1200. 5% of $1200 is $60, so their contribution is $60. Week 2, their pay is $900. 5% of $900 is $45, but they affirmatively elected to have $50 withheld, so their contribution is $50.
For the participants who want to defer the annual limit, they will already be making an affirmative flat dollar election each year, so the auto-escalation will not apply.