Reading the answers to previous questions regarding SharePoint alerts, I have found many interesting information on how to define a custom template, for example: this article
But it looks like such customizations will actually erase the default template and impact the whole farm. Is there any way to deploy a custom alert template to only one site collection?
According to the docs for STSADM -o UpdateAlertTemplate you can use the -url param to target a particular site collection
stsadm -o updatealerttemplates -url <Specifies the URL name to a site collection.> [-filename <file name>] [-lcid <language>
Alert Template is just a Workflow. Create your custom workflow in SP Designer or through Code and install the workflow only in that Site template.