Any way to modify .msi service files before installing program?

Im sick of program developers adding a bunch of extra services with an application.

My question is, can i modify a .exe program file so I can pick and choose which services I want to install with the program?

For example:
1. I downloaded itunes64setup.exe
2. I opened the archive with 7zip to reveal all the .msi files packaged with the installer
3. Applesoftwareupdate.msi is something that I purely do not need.
4. But when I go and delete it, or try to, an error pops up stating that it's a read only file.

Is there a program that will let pick and choose which service files I want to keep and let me edit the installer file?

I have no idea if this could help, but I've used it to replace/modify application logos/icons to my custom made ones.

http://www.heaventools.com/overview.htm

try fully extracting to a folder, uncheck read only on update apps propertys / delete, repack as .msi

can you add msiexec commands to the msi files before repacking?
If yes you want to look into this.

https://technet.microsoft.com/en-us/library/bb490936.aspx