I'm using sendTransactional() to send emails programmatically. All working fine besides the following line in the email template is not included
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I found it out. It has to include ->setDesignConfig()
So the following code will include CSS file when sending out emails with sendTransactional().
Mage::getModel('core/email_template') ->setDesignConfig(array('area' => 'frontend', 'store' => $storeId)) ->sendTransactional($templateId, $sender, $recepientEmail, $recepientName, $vars, $storeId) ;