It's perfectly possible to accomplish this, and it doesn't even require any messing about with the SEPM.
Presumably, you have older 12.1 client package exported which already behave the way you need. All you need to do is grab the below files from the older packages, and place them in the new SEP client version's directory:
These control how the installer behaves and what it installs:
- setAid.ini (http://www.symantec.com/docs/HOWTO81039)
- Setup.ini
This controls which SEPM the client will connect to, and which is the preferred group:
- SyLink.xml (http://www.symantec.com/docs/HOWTO55047)
It should be fairly simple to write a script to copy the 12.1RU3 client installer a few times of times (i.e. the SEP and SEPx64 folders inside the Part1 download from FileConnect), and paste the above files (taken from an earlier exported, known-working, client package) into the new copies to replace the existing files.
Note: These should be what you need, but will produce client install packages that are not bundled into a single executable.