I haven’t tried messing with the filter settings but it looks like you’ll have a couple properties to set. Namely, setting SPAlert.Filter and some options in SPAlert.Properties.

I would recommend asking your question on SharePoint.SE if you need more help.

Thanks,

Kit

Kit – How can one set “Send Alerts for These Changes 
Specify whether to filter alerts based on specific criteria” programmatically? Please advise. Thanks. – Mark Kamoski