So, from what I can tell, the first In-Reply-To references the Message ID.
You can see this by sending an email to your Gmail account and sending a reply.
Then, click on the three dots for each message in Gmail and choose “See original.” The very first line at the top shows the message ID.
If you look at the headers in the reply, you will see that the “In-Reply-To” Matches the Message-ID of the first message. That’s what you need. Then, whenever you create a reply, you should be using the Message ID of the email you’re responding to.
I haven’t had time to test it yet, but that’s the mechanics. I don’t think you can do this with the GMail module, but the email module should work.
You could make a suggestion to the Make team to add this.
If you’re still having trouble doing it, let us know.
L