You are giving them a cut partly because your application will contain parts of their source code. I think it's not a good/exact comparison.
I think the ownership is about the output format, not the contents itself, so it could be better compared to InstallShield, for example. It is used to package and easily distribute/install your Windows programs.
If it was free but they'd requested similar conditions to those in the iBooks EULA (that you can only distribute it in their own channels, that they might reject your program if they don't like it, etc.), would you still consider them for distribution?