The documentation on the hostname parameter in alert alertactions.conf is a bit ambiguous on behavior for default ports on http or https but based on the documentation you can use the [protocol://]host.domain.com[:port] format to set the link base, in alertactions.conf which is presumably what gets edited as Link hostname when you go to settings->general settings->email settings in splunk web.
I would try there or in the config and specify the deisred base in protocol://host.comain.tld format. (e.g. https://splunk.mydomain.com )
Try running this on your indexers and look for hostname to confirm that alert_actions.conf has been reloaded and that no other location is clobbering your setting :
$SPLUNKHOME/bin/splunk btool alertactions list --debug