I don't know how this would affect the hot-standby engine, but you can directly edit the SQL in the TriggerQuery and ResetQuery colums in the AlertDefinitions table.
These values are only updated when the alerts are edited in the GUI, so you will need to update it whenever the GUI is used on that alert.
I do this for custom free disk space alerts so that I can specify megabytes as a custom property rather than bytes.
Thanks for the tip smargh! It took us a little while to work out the right alert conditions for the triggerquery but we have it working now. Works great!