Yes, in fact you can do this

Excluding yellow colors would be challenging, as I am not good with hexadecimal color manipulation, but assigning one and same color to all layers is much easier. The key to achieve this is to use Javascript to manipulate the Flash Authoring Environment (i.e. inside Flash, where you draw, code, create layers, etc.). We can then, by adding a new button to Flash, allow it to change all the Layers' outline color to be changed to a specific one.

Start by opening a Flash JavaScript File (from the list you choose Actionscript 2.0/3.0 Document from), and type this:

Code:
var layerArray = fl.getDocumentDOM().getTimeline().layers;

for(i in layerArray){
	layerArray[i].color = "#FF0000";
}
and save it as something like, Same Color Layer.jsfl. Next, go to:

C:\Users\your_username\AppData\Local\Adobe\Flash_version\language\Configuration\Commands

make sure that you have enabled displaying of hidden files and folders (to do this, while in Windows Explorer, press Alt to bring up a menu, move to Tools, and click on Folder Options. Switch to View tab, and under Hidden files and folders, make sure it's enabled) in order to navigate to the specified location.

Move your .jsfl file to the Commands folder, and you don't need to close Flash as it will automatically refresh the commands list.

Then, create a new Flash Document (AS2/AS3), create some new layers, and in the Top Menu, move to Commands, and click on the button with the same name as your .jsfl file (Same Color Layer). If done correctly, it will change all the layers' color to red (you can of course change the default color inside the .jsfl file, by changing the hexadecimal value).

This will only change the colors for layers in the current active timeline.

However, I'm not sure your magnification request is possible, at least not with the pre-made functions in Flash for Authoring Environment extension. The same goes for setting Short as default. At least your main request was filled, right :P?

Hope this helped