Yes. This is fine. As you note, the appxupload's format is documented as being a zip archive containing the .appx and .appxsym files, and the .appxsym file is a compressed file with the app's public symbols. The appx and its creation is documented in App packages and deployment
Generating this yourself or generating it through VS will give essentially identical results, barring differences in the appxupload's contents (most likely different appx options or processing).