Final Answer
On the webpage
https://partner.microsoft.com/en-us/dashboard/Registration/Hardware?step=SignUpload
I also got the error message:
We encountered a problem processing the file you uploaded. Please ensure the file you sign and upload is the same file you downloaded.
In the end, I signed my file wrongly.
My main problem was that the /ac commandline parameter was missing.
The command that worked for me for signing the file SignableFile.bin is
signtool.exe sign /v /fd sha256 /ac "<PATH TO ROOT CERTIFICATE G2 .cer FILE>" /s my /n "<ISSUED TO NAME OF YOUR USER CERT>" /t http://timestamp.digicert.com .\SignableFile.bin
Good luck to any future reader