My knowledge of windows installer is by no means comprehensive, but I do know a bit. All you actually NEED to run a windows installer package is the .msi file. These are essentially executable, in that the MSI files are run by the windows installer program. All the other files created (the .ini, setup.exe, and the two bootstraps) are meant for people without windows installer on their machine.
Windows Installer was first packaged with Windows 2000, and that version has been included with every Windows since (ME, XP). However, with .NET there came an updated version of it, so users need this updated version to install packages created with the .NET Setup and Deployment project wizard. This is why people usually include the bootstrap, because without it users wont be able to run the install package.
However - I dont bother with the bootstrap, because when I deploy applications I rely on the fact that dotnetfx.exe (the .net runtime redistributable) installs the latest windows installer on to the machine. I use an autorun menu to give the user two choices, to install the .net framework and then install my application. Once the .net framework is installed the windows installer runtimes will be updated and they can run my .msi file.