I won't comment on 3rd party setup packaging tools because I don't use them myself. However I am pretty sure that the old PDW that was replaced by Visual Studio Installer 1.0 and then 1.1 (back in the 1998 to 2000 timeframe) can only create per-user setups.

If you were to use VSI 1.1 you have the option of choosing either per-machine or per-user as the default, and overriding this via the command line if desired when you actually install.

You might take a look at:

Per-user Installations

Per-machine Installations

Specifying a Per-User or Per-Machine Installation