You can customize the URL used in Go To Ticket links under Configuration\General Settings, but there is no option at the moment to customize the position of the link.
If you are mostly interested in displaying these links in automated emails, you could disable Go To Ticket links under Configuration\General Settings and add your own preferred links to the actual contents of your outgoing email templates under Configuration\E-mail Settings. If you manually add the links to the templates, making use of the ticketid parameter for outgoing email templates, you can choose the position of the links. With Include Links To Web Interface disabled under Configuration\General Settings though, Go To Ticket links would no longer be included in manually sent emails.