Sometimes I speak code better than english 
Thats totally fine from the point of view of algorithmic thread calculation, from my interpretation of
https://www.jwz.org/doc/threading.html
Apparently, the real length of the References-Array does not matter. From my experiments however the order matters. The last referenced (“`reply-to’”) post should be the last.
It seems to me that there is some doubt of whether it makes sense to take advantage of email-readers ability to reflect “hierarchies” and the (simplified) tree-nature of replies visually (which can often be switched off by the email-client anyway). I dont have that doubts 
@zogstrip wanted to look into this and I would be glad if we help the email-clients to visualize what happened - especially when reply-by-mail is offered imho it makes sense to give the users the possibility to see to which post/mail was replied to. Again, the change should be extremely cheap code-wise and results in an increased usabilty. And users who dislike to see deeper threads in their mail-client (if such users exist in a larger number that would be a surprise for me) can usually switch threaded-views off.