Its probably that variables defined in AUTOEXEC are "global" scope, i.e. can be referenced in any other batch file, but variables defined within a batch file other than AUTOEXEC only exist within the scope (context) of that batch file. But, I haven't tested this...

I think in DOS they were all global in scope. SETLOCAL appeared with Windows NT (cmd.exe), not sure which version (I didn't use the early ones).