Spooner's apostle's train makes scheduled stop (4,2,4)
I believe the answer is:
port of call
'stop' is the definition.
The answer and definition can be both locations as well as being singular nouns.
Maybe you can see an association between them that I don't see?
I can't explain the rest of the clue.
Can you help me to learn more?
(Other definitions for port of call that I've seen before include "place to stop en route" , "Place briefly visited" .)