Tigerdude,
First of all. When I build a plane I completely assemble the plane BEFORE I cover it, so covering over the tri-stock is not a problem at all. But in your case, what is wrong with applying a small piece of covering over the tri-stock after you attach it? Nobody will even notice it unless they are looking for it.

As for the servo tray. Once again, I think that you are "over engineering" the kit. There are places in some kits that I will change the way things are done in the instructions because in my experience they way they do it isn't the best way it can be done. But in the case of the servo tray I look at the thousands and thousands of pilots that have snaked out the servo wire the same way you are trying to avoid and have never had a problem with it. I've had more planes than I can count with the servo wire like that and I've never had a problem with it at all. I'm going to be ready to do that portion of the kit this evening and so far from what I can see I don't see any reason to do it any differently than the instructions call for.

Ken