I spent some time trying to figure out how to get the provided .desktop file to work correctly in GNOME. When a non-absolute path is used in the desktop file, you need to specify StartupWMClass in order for gnome-shell to know that a running application matches one in its desktop database. I also set a version and removed the deprecated Encoding field. With these changes, the desktop file passes desktop-file-validate cleanly.
P.S. I found this while working on a new spec file for Bitcoin, which you can find here: https://github.com/eklitzke/bitcoin-copr/blob/master/bitcoin.spec . I plan to contribute this work back upstream as well, once I've figured out more of these packaging issues (desktop files being one of them!).