There haven't been any posts to this thread for a while. I started poking at this again today. I ran into the same problem that Henry did--the fact that a package_id can vary from installation to installation.
Then I discovered that ad_parameter will still look at a parameter file, even though it's deprecated. So this solves about 80% of my problem (how to set some systemwide parameters outside the parameters table so they can be different for us depending on who is running the aolserver instance). Joy!
When doing the research on this, I realized that lots of ad_parameter calls don't include a package_key. I think all the ones that don't are pulling parameters for the acs-kernel package_key. Shouldn't those calls say things like
[ad_parameter AllowAdminSQLQueries acs-kernel 0]
instead of
[ad_parameter AllowAdminSQLQueries "" 0]
?