Nicolais Tip got me on the right track; Here is the working code:
// add a query_var first
add_filter("query_vars", function($vars) {
$vars[] = "myTheme_podcast_time";
return $vars;
});
add_filter("rewrite_rules_array", function($rules) {
$newRules = array();
$newRules["(.*)/time/([\d|\:]+)s?$"] = 'index.php?name=$matches[1]&myTheme_podcast_time=$matches[2]';
$merged = array_merge($newRules, $rules);
return $merged;
});
And then in single.php
:
$time = get_query_var("myTheme_podcast_time");
// do stuff