First, please don't flame me...there is a really good reason why I am asking this (pertains to my job).......
As for the question, is it possible to extract the contents of a MSI file, then replace/inject files to contain spyware/adware/etc. then package the msi file back to normal so that it looks "normal" or unchanged? Will windows installer recognize this and not allow the loading of the files, or will it continue on its merry way?

As an example...one would have a MSI file, replace some dll files for instance which are the same name, just different file contents, repackage the MSI and distribute it.