Prorate the initial payment of a membership while using PMPro Set Expiration Date.

my_pmpro_custom_prorate.php

<?php

// Copy from below here...

/*
 * Prorate the initial payment of a membership while using PMPro Set Expiration Date.
 *
 * For year-long proration cycles, leave as is.
 *
 * For partial year cycles (such as classes between September and May), change $days_to_prorate to the number
 * of days between the start and end of classes.
 */
function my_pmpro_custom_prorate( $level ) {
	$days_to_prorate = 365; // By default, prorate the entire year
	if ( $level->expiration_period === 'Day' && $level->expiration_number < $days_to_prorate ) {
    // Multiply initial payment by how far we are in the prorating period
		$level->initial_payment = $level->initial_payment*($level->expiration_number/$days_to_prorate);
	}
	return $level;
}
add_filter('pmpro_checkout_level', 'my_pmpro_custom_prorate', 11, 1);