This is a metadata thing, and the send-to-kindle application will insist on doing its own thing.
You can always use the email option within calibre itself (under the Connect/Share toolbar icon), which will allow you to email the books using your email account. You will have to add your email address as allowed in your Amazon account settings. emailing the book will use only the metadata in the file.
Note that when adding books to your online Personal Documents, Amazon will post-process the book and make covers work regardless (and override the sharing setting). Also, you cannot send an AZW3, if I remember correctly they will simply convert it to the legacy MOBI format.
People have had luck emailing a dual-mobi, but then covers disappear.
Personally, I've always found it easier to directly sideload everything.