It's a good idea to add :tumbleweed: smile to this forum
I spent 3 days for searching answer and making experiments. So, as a result:
1) To pass MacOS Gatekeeper I should use apple developer certificate.
2) I could change content of signed .app file as I wish. I don't try it with my own app because my certificate is not ready yet, but I successfully change contents of few other signed apps - no issues with running was detected. Maybe there is any problem with my understanding of signature..
Helpful links:
How to sign your Mac OS X App for Gatekeeper | Successful Software