If the application files are stored inside the msi file this means that they are packaged in one or multiple CABs which in turn get streamed into the msi file. They don't appear in the MSI database but are placed in a separate stream.
You could try a compression tool to delete the file. I know that 7zip can open msi files and CABs inside the msi, but I don't think it can delete the file.
Note that this would invalidate any digtal signature of the msi file.
Alternatively, run the msi in adminstrative install mode (/a) which will unpack all the application files and give you a smaller .msi file. You can then use this with external files.
Stefan Krueger
InstallSite.org