MIME Headers Not Making it Through Gmail API

Actually, it's a lot simpler than that! If you just supply the correct Subject in the headers, and the correct threadId in the body, Google will calculate all the references for you.

new = MIMEText("This is the placeholder draft message text.")
new["Subject"] = "Example Mail"
new["To"] = "[email protected]"
new["From"] = "[email protected]"

raw = base64.urlsafe_b64encode(new.as_string())
message = {'message': {'raw': raw, 'threadId': "14ec598be7f25362"}}
draft = service.users().drafts().create(userId="me", body=message).execute()

This results in a draft, ready to be sent in the correct thread:

Then, I send the mail. As you can see, the references are calculated for you:

MIME-Version: 1.0
Received: by 10.28.130.132 with HTTP; Sat, 25 Jul 2015 07:54:12 -0700 (PDT)
In-Reply-To: <CADsZLRz5jWF5h=6Cs1F45QQOiFuqNGmMeb6St5e-tOj3stCNiA@mail.gmail.com>
References: <CADsZLRwmDZ_L5_zWqE8qOgoKuvRiRTWUopqssn4+XYGM_SKrfg@mail.gmail.com>
    <CADsZLRz5jWF5h=6Cs1F45QQOiFuqNGmMeb6St5e-tOj3stCNiA@mail.gmail.com>
Date: Sat, 25 Jul 2015 16:54:12 +0200
Delivered-To: [email protected]
Message-ID: <CADsZLRxuyFhuGNPwjRrfFVQ0_2MxO=_jstjmsBGmAiwMEvfWSg@mail.gmail.com>
Subject: Example Mail
From: Emil Tholin <[email protected]>
To: Emil Tholin <[email protected]>
Content-Type: text/plain; charset=UTF-8

This is the placeholder draft message text.