It annoys me that I then don't get to observe the full paths with lsbom once the package is installed.
Your life will be MUCH MORE PLEASANT (and robust, hint hint) if you pretend that lsbom and package receipts DO NOT EXIST.
Here's three good reasons:
1) BOM files change format from time to time, and contain LOTS of stuff you don't want to care about.
2) Installation package receipts change format from time to time, and sometimes include destination paths that are supposed to be pre-pended onto the output of lsbom. Thus, lsbom does not always give you the whole story anyway.
3) It is not that much work to write your own preference file containing a list of files installed and a destination path.
Here's a sketch:
a) during your installer build makfile, pipe ls $MYINSTALLATIONROOTDIRECTORY into FOO.PKG/Contents/Resources/MySpecialBomFile, then
b) during your installer's postflight, mv this into /Library/Preferences/com.myCompany.myGreatApp.BOM and prepend the custom location as line 1. (Or you can be all FANCY and use a plist file or something.)