But the form interface for the settings does not depend on the options stuff. It only creates a table with the settings in it that I want to show to the customer. There are methods called that I have to implement with the code that creates the parts of the form. So there I am totally free as a developer.
The magic happens after the selected settings are committed by the customer. And I agree with you that there is a feature missing where I can tell the wp-admin/options.php that the committed stuff is for the site or the blog. That's the only missing piece, I think.
As a solution I would, in a first step, change the behavior of my settings to be saved for the blog only. In a second step I would implement a posibillity to set some site options and request a feature for the next WordPress version that would implement such a method for everyone. Something like: send the form to options.php and save it for the blog or send it to site_options.php and save it for the whole site. So you can use the the same settings api for the forms and only have to decide which kind of settings you would like to save.
If blog options override site options or the other way around depends on the developer of a plugin...
What do you think?