This can be accomplished by running through the Download Only process multiple times, once for each operating system.
Start by creating a separate folder for each operating system that you would like to download the installation files for. For example, if you need to download for every operating system, create four folders:
Then, run the MATLAB installer and use the Download Only option. Select the first folder (Windows-64-bit) to download the files into. Then, only select the 64 bit Windows files to be downloaded. Allow the installer to proceed and download the files.
Then, run the installer again and use the same process, selecting the Windows-32-bit folder, and allow the installer to download the 32 bit Windows files into that folder.
Repeat until you have done this for each desired operating system. You will now have a separate installation folder containing only the files required to install MATLAB on each individual operating system. Provide these installation folders to your users based on the operating system that they are using.