I created a new package and needed to add some code to the _Layout.cshtml file and the _ViewStart.cshtml files. I proceeded to create the files with the same names but with .pp extension (.transform is only for web.config as I understand, the site does not clarify).

I noticed upon deploying the package that none of these transformations were performed. Then I also read in STackOverflows that the .pp are meant for new files???

You're correct. .pp is meant for new file only.

There is currently no support in nugget to add code to non-XML file.