Nearly all free software licences require the preservation of existing copyright notices. If the author of a piece of GPLv3 software accepted your modified version, then since this code had to be conveyed under the terms of GPLv3, the author is required to preserve your copyright notice.
Nearly no free software licences concern themselves with the minutiae of source-code control systems, so nearly none of them make any reference to "commit messages" or "history", nor are there any requirements to preserve the artefacts of a particular source-code control system. This is unquestionably a good thing, since otherwise projects would be full of
foo.c,v files we could never remove.
You should go back to the author, apologetically point out that GPLv3 s5a required you to add a copyright notice to the file(s) you modified (and in which you now have a copyright interest), and ask if you could add those in a separate pull request. Strictly speaking, the author isn't obliged to accept them, but most people in free software understand that the copyright notice is the standard currency of acknowledgement - and that source-code control system artefacts aren't.