I believe this behaviour transferred from the original Nylas mail client to Mailspring.
I would like to be able to reply to an older e-mail in a conversation by clicking on it and using one of the reply shortcuts (A/R) to actually reply to that specific e-mail. This is useful if the conversation spread out to two separate threads with two participants, and you want to follow up on an e-mail with one of the earlier participants in the thread instead of who you wrote to last time around.
So far, no matter what e-mail in a conversation you open and click on, when you hit the reply shortcuts, a reply to the most recent e-mail and their participants is being created.
(Originally posted by enoversum on GitHub.)