Every share (folder) is independent of other shares, so yes you would need .stignore in every folder
Because of my example. In general included files may reside elsewhere, but you need to point to them relatively to the root of this particular share's folder.
Documentation specifies that included files should reside in the folder itself, or it subfolders:
Note that while this can be used to include patterns from a file in a subdirectory, the patterns themselves are still relative to the folder root.
So regarding placing it in /home/user/whatever , completely outside the shared folder - I'm not sure about it, but you should give it a try, it may just work.
If the above works, I guess a single ignore template file may be used for many shares. Just sometimes people want to exclude different things from different folder pairs.
If using single location won't work due to some implementation limitation or access rights, it's not that big of a deal, you can always copy-paste ignores upon folder creation.