Date #return_value to ordinary time()
For what it's worth you have a typo in your sample code, $startDate is being referenced as $startDatea - note the extra "a". As for a shorter version, try:

$startDate = variable_get('start_date', NULL);
$startDate = date('Y-m-d', mktime(0,0,0, $startDate['month'], $startDate['day'], $startDate['year']);


I suspect not jumping from numeric to string and then back again might save you a few cycles at the PHP layer.