I don't think I've ever had a partial download.
I've tried a test which may or may not throw some light on what is happening:
1) At 22:16 yesterday I sent an email from one of my little used accounts to my main account.
2) At 22 :27, I established that it was waiting on the server but did not download.
3) At 22:37 I sent an email from my main account to the other four accounts and having checked that all four had arrived (so now five waiting to be downloaded) put the Mac to sleep.
4) At approximately 23:00 I woke the Mac but no mail downloaded so I put it to sleep again and went to bed.
5) When I woke the Mac this morning, all five mails (plus one other that had been sent by someone else early this morning) downloaded.
Using the columns Date Sent and Date Received, I see that all those mails show the time sent as the time I sent them and the time received as either the same time or a very few minutes later. If the time in the Date Received column is the time received by the server rather than the time my copy of Mail received them, then this is correct.
It seems the length of time asleep may be of relevance.