Hi Joe,
This isn't really an answer to your question but it is the path I'm taking to solve this, and other, issues.
This what I "believe" is the process:
When the SEPM exports a package it dumps all the files it needs into a directory, runs a utility called Packlist against the directory to generate the packlist.xml which seems to be a list of all the files in the package and their checksums, etc...
After Packlist is done the whole directory is zipped (using parameters I'm not sure of). The zipped file is then run through an SFX generator called MakeSFX (again using switches I'm not %100 sure of). What comes out the other end is the Setup.exe installer package.
What I have been trying to do is breakdown the SEPM packaging process so that I can do a few things, 1) update the virus defs, 2) update the IPS sigs 3) modify setAid. Then repackage manually using the programs above.
I have made some progress, but I'm not all the way there.
I would imagine that the steps above using packlist and makeSFX are security measures put in place by Sygate to help prevent bad guys from compromising the install package.
If there is an easier way to create a modifed package, I'm unaware of it.
Someone had mentioned to me that in the SEPM you can "Add Client Install Package" and point to a directory with all the modified files...but when I've tried, I get an error about a duplicate name. I don't want to delete my standard packages, I just want to add a new one or two with custom settings.
Hope this helps,
-Mike