I am assuming that you specify these on the specific collections getting crawled and indexed, but just to check.
If a Meta Collection is made up of a number of Web Collections, should the kill_partial file be on the specific Web Collections rather than the Meta Collection?
Your understanding is correct - the kill_partial.cfg affects how an index is built and must be applied on the underlying datasource collection rather than the meta collection.
A good rule of thumb if you’re unsure is:
If the change is applied at index time and affects the index build - set this on the data source collection(s)
If the changes is query time and affects how a query runs then set this on the meta collection