Yes. You can call EngineRunner from one of your install scripts to check and see if there's a new version of the package that's installing. Actually, this is exactly how MacFUSE's autoinstaller works (
http://code.google.com/p/macfuse/wiki/AUTOINSTALL). MacFUSE uses a binary called "autoinstaller" because it predates the EngineRunner command. But MacFUSE's autoinstaller binary compiles in the Update Engine sources and basically does just want EngineRunner does. Take a look at how MacFUSE uses its autoinstaller (you'd likely use EngineRunner) from its mpkg.
HTH,
G~