I ran into this issue myself. In order to get the custom property to pass into the alert I had to build out the following variable:
${SQL:Select SupportGroup from APM_ApplicationCustomProperties ACP JOIN APM_AlertsAndReportsData A on ACP.ApplicationID = A.ApplicationID Where A.ComponentID = ${ComponentID}}
You should be able to use the same thing just change the property name to yours and on the where use A.ApplicationID = ${ApplicationID}.