>A decision in GUI design can NOT be taken without considering its >implications on the UI design side, and vice versa. I believe this is a faulty statement. If anything a good UI Design drives or serves as a base of the graphic design and it definitely shouldn't be vice versa.
Let's not forget that before the interface is designed, persona(s) should first be established, and their goals outlined. Without establishing goals, we would most likely end up creating an interface that represents the implementation model rather than the mental model. With regards to what stage the graphic design plays a role, it depends on the product being developed. We already know that Haiku will contain the same widgets as BeOS and pretty much every other established interface such as Windows and Mac OS. This would allow the graphic design work to start on the simple widgets like the checkboxes, and radio buttons. As for the placement of these widgets, and what action(s) they perform, this would rely heavily on the interaction designer.
Your blinking menu item example leads me to several UI design questions: Why is this really needed? Is there a better way to achieving its purpose? Are they assuming the user is too stupid to realize what they selected? Isn't that quite insulting? How often does a user even pay attention to the blinking? What kind of delay does it have and how does it interrupt the flow of the user's tasks? From a graphic design point of view, it is an effective way to notify a user of what they selected and is a neat effect. I don't think this makes it a good UI design though. If anything, it sounds like a legacy UI feature they were forced to keep.
From an interaction design perspective, this is simply visual feedback, informing the user as to what they selected. It is a very fast blink that doesn't take up more than a split-second, and I personally find it unobtrusive. I navigate interfaces rather fast, and this has let me know (on multiple occasions) that I have selected the wrong option before the next window (or event) is even loaded. This gives me a heads-up as to what I should expect next, and allows me to plan ahead on canceling the action. If you want to insult the user, simply bombard them with "Are you sure?" dialog boxes, and distracting balloon popups letting them know they have unused icons on the desktop.