Use a wrapper to run amnesia-security-check after sleeping 2 minutes.

config/chroot_local-includes/home/amnesia/.config/autostart/security-check.desktop

@@ -2,7 +2,7 @@
 Name=amnesia-security-check
 GenericName=check amnesia known security issues
 Comment=check amnesia known security issues
-Exec=/usr/local/bin/amnesia-security-check
+Exec=/usr/local/bin/amnesia-security-check-wrapper
 Terminal=false
 Type=Application
 Categories=GNOME;X-GNOME-PersonalSettings;

config/chroot_local-includes/usr/local/bin/amnesia-security-check-wrapper

+#!/bin/sh
+
+sleep 120
+exec /usr/local/bin/amnesia-security-check