> [...]
> I understand it makes no sense to try to get
> /gnu/store/greenclip.service, but would it be possible to achieve
> /gnu/store/pznbc8xxhfkwxjbaff9h982cy4df1y1a-greenclip.service/some-directory/greenclip.service?
> Or are files always saved at the "top level" of the store?

It is possible with file-union. See the G-expressions section in the
manual.