The .exe needs the runtime engine to work. You can install the runtime engine separately, but it has to be installed. Then all you have is essentially an installer the size of your build. The advantage of including the runtime engine in the installer is that it is the correct version for your build.
The uninstaller is part of the build. As long as the GUID is the same for your build, newer installs will uninstall the old program first.
If you want to keep the distribution small, don't include the runtime engine, but still create an installer.
Include instructions on how to download and install the runtime engine from the NI web site. A given machine can have multiple runtime version installed concurrently. All versions are available with direct FTP links that you can communicate to your customers.
Some of the files created by the installer are not really needed and you can typically create a sub-megabyte distribution by keeping only the essential stuff. For example if the users install the correct runtime first, it is guaranteed that the correct MSI installer is present and you can leave out InstMsi.exe and InstMsiW.exe for an additional saving of about 3MB. 🙂