I can't comment on the gate valve on the return line. I just don't have experience with it. I don't know why it is necessary. Does it put extra strain on the return pump? Reduce its life span? To match the skimmer flow rate?
!!!!!!!!!!!!!!!If both your surface skimmer heights are the same, then you will have water over flowing into both overflow boxes in equal amounts. Right? The purpose is to have all the water going into your primary drain with the gate valve on it. The backup is a backup for a reason, and it is normally located within the same overflow box as the primary in case the primary gets clogged and your wated level rises.!!!!!!!!!!!!
Eliminate the Emergancy overflow box. Put both drains in one overflow box because that is how it will work most effectivly.
You might shorten the drain pipe in your overflow box, and then adjust the level of water with the gate valve. That is the idea. If it is to tall then you can still get the vortex.
Also, if you make your drain pipe detachable, you know pressfit (no glue) maybe even threaded, you can always make an adjustment to the drain pipe height. You can still remove it, sawing off a little more and shorten it until you reach a desired length.
------------------I would be carefull keeping the skimmer out of the sump, especially with your return going directlly into it.
First, can the skimmer handle the complete flow of the tank, with out water comming out of the top of the skimmer? Maybe that is what the gate valve on the return is for, but it seems like a lot of things need to happen right all the time in order for it to work.
Things in a tank can change, flowrates, bulid ups inside the pumps and tubes
Second, what happens if you have a skimmer over flow just due to anything happening randomly. Many people have come home to an over active skimmer before and thanked the aqaurium gods that our skimmers were in the sump.
Third, back to skimmer flow capacity. When the power shuts off can the skimmer handle all the flow easily from the tank? If it can handle it when the power is on then I am sure you are ok.
I know I repeated a lot, but some things are worth repeating.
The most important thing is your baffling. Once you have a baffled system where the area in which the drain pipe dumps never changes levels then you are set since the water level should never essentially change in that area where you have your drain pipes. I have my skimmer gravity fed using the Herbie method without any problems. 
