What you would normally do in a safeboot deployment is have a machine group thast contains the majority of your machines. You would assign all the users that could possibly use these machines to the group, then you create the install set and roll out. You could one to one map the users to machines but it would be a pain to do for lots of users.
Configuration can be based on both users and computers seperatly. Users are usually pulled in via "connection manager" which looks in active dircectory, but as you have stated you dont have AD, you can just enter the users manually into the console and assign them to groups.
You could also manually create the machine registrations and assign the users prior to software install on the clients.
Another method would be to have a batch job (or custom executable) kick-off the SafeBoot installer (without auto-restart; include sbadmcl.exe and sbadmdll.dll in fileset), then pass control back to the script utility to prompt for user ID(s). Once script has list of users, it could register its hostname as a placeholder and assign users to it. The script should then initiate a reboot.
Once the machine boots back up, it will discover the unused registration, activate it, and pull down the associated users.