If you look in Register.php, you'll see this code:
// We'll do custom fields after as then we get to use the helper function!
require_once($sourcedir . '/Profile.php');
require_once($sourcedir . '/Profile-Modify.php');
At this point, the values are in the database - but honestly you are not recommended to mess with that part of the process (since it's just reusing the profile code), instead query it from the smf_themes table at that point (since you'll have the new member's id) and can do whatever you need to do right then.
Essentially, SELECT value FROM smf_themes WHERE id_member = $memberID and variable = 'cust_fieldname' (but I know you know how to write mods and thus can properly use $smcFunc instead of just mashing the query in there)