The signature of the binary is invalid but codesign says otherwise

What does spctl say?

The standard reference for these issues is: https://developer.apple.com/library/archive/technotes/tn2206/_index.html

The most common cause of problems like this is that you have nested code in the wrong location. Nested code should be placed according to the rules outlined in the Nested Code section of Technote 2206 macOS Code Signing In Depth.

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—
Quinn “The Eskimo!”
Apple Developer Relations, Developer Technical Support, Core OS/Hardware

let myEmail = "eskimo" + "1" + "@apple.com"

If the app is signed correctly on your computer, make sure the zipping command you are using is not destroying the UTF8 encoding and the signature is then seen incorrectly on your submission to Apple.

When preapring the zip archive for notarizaion use ditto and "–sequesterRsrc" option.

/usr/bin/ditto -c -k –sequesterRsrc --keepParent "$APP_PATH" "$ZIP_PATH"

Regards,

Conor

Answer from Bruji solved my problem. Thank you.
But there is a small mistake in the command. There should be two dashes -- (minus symbols) in front of sequesterRsrc

Code Block 
/usr/bin/ditto -c -k --sequesterRsrc --keepParent "$APP_PATH" "$ZIP_PATH"

There should be two dashes -- (minus symbols) in front of
sequesterRsrc

This is more evidence that you have nested code problems. Except under unusual circumstances, like shipping an Automator action, a code signature should end up in resource fork. If it does, it’s commonly because you are signing data as code, which is not a good look.

Share and Enjoy
—
Quinn “The Eskimo!” @ Developer Technical Support @ Apple
let myEmail = "eskimo" + "1" + "@apple.com"

Thank you, @Bruji. This solved my problem too.