You're still confusing the logo program with a file format. Yes, developers need to sign a licensing agreement to use the logo. But I don't need to sign anything to create a universal binary. And licensing the logo doesn't involve any certification by Apple.
I thought I understood your point about Xcode up until the last sentence. Then you lost me. I don't know what you mean by:
That is the trade-off you accept when you opt for a multi-platform development tool.
Did you mean single platform instead of multi-platform?
I thought you were making a point about open source tools versus proprietary tools.