This was answered on Github, answering here too, for folks future reference.
To use the SMTPAPI to substitute for subjects, you'll need substitution tags in the subject of the email and then include the x-smtpapi
header with substitution tags defined.
Using the SendGrid SMTPAPI Library:
<?php
...
$message->setSubject('[sendgrid-php-example] Owl named %yourname%');
$header = new Smtpapi\Header();
$header->addSubstitution("%yourname%", array("Mr. Owl"))->
...