The limited edition of InstallShield targets building single Windows Installer projects. You could almost make a single MSI that has all those contents, and chooses which to install, but I don't think the limited edition exposes enough of the controls that you would need to use - you can condition files by OS, but I don't believe you can condition them by .NET framework version. Additionally this doesn't sound like the architecture you're hoping for.
If you have budget to consider the premier edition of InstallShield, the Suite project is designed to handle the installation of several packages, and they can be conditioned however you like. If you only have the budget for the professional or express edition, the professional edition can definitely offer the single MSI approach, and the express edition may as well.
(But don't take my word on the edition differences too far; I spend all my time in the premier edition, so I forget what the lower editions' exact capability sets are.)