There are no settigns on the client for changing the codebase given from the server (but there is the client network settings that can append DNS suffixes in order?). I expect if you try to change it via scripting on the client it just wont stick and will revert often.
You might wish to examine the codebases in the database and try to change those, but the same thing will occur, they will revert, so not sure how to do this within CMS, although have never faced this problem yet, it's typically not somethign Altiris is designed to do, to work around a DNS issue, but an idea posted might help you.
Perhaps a sheduled client task script that takes the codebase from the policy.xml, converts it as you wish and then appends to the hosts file? I could probably manage that with autoit unless the change to the suffix was dynamic since i am not au fait with where the source for that info will be found from the client side. Logon script may also help.