Difference/Relationship between Filter section in AlertTemplate.xml and Filter Property in SPAlert class

In regards to SharePoint 2010, I'm having trouble understanding the relationship/difference between the Filters/FilterDefinition section in the AlertTemplates.xml schema file, and the SPAlert classes Filter property.

Am I correct in assuming that the AlertTemplates.xml file will define the Filter for all new alerts created by users (assuming the AlertTemplate applies for the particular list/library)? I notice that all SPAlert objects created at this time have an empty value for the Filter property.

What then is the reason for the Filter property in the SPAlert class? If this is later populated (for example, programmatically), does this then override the original Filter from the AlertTemplate?

Thanks for helping me understand, cheers in advance!