The problem with that method is that there are two flew sections on that up-pipe. Since the egr cooler is gone the weight of the pipe will sag and end up breaking the flex pipes. We were doing a similar method back in 2005 and was having all sorts of flex type cracking issues. If you delete the whole egr cooler then you have to delete one of the flex sections.
I don't get it, just weld a freeze plug in both ends of the egr cooler, put it back in and you are done, no cutting and still appears factory. Problem solved for less then $1 if you know how to weld.
There are only two main benefits of removing the egr cooler:
1. remove the exhaust flow from the coolant so that the coolant isn't flash boiled.
2. the cooler can crack and leak. Thus allow coolant into the manifold or through the egr valve and into the intake.
One benefit of a full delete over any simple welding is getting the modified up-pipe without the scoop. You have to remove the scoop in the up-pipe on 2005 and newer trucks!! You can always go junk yard hunting for a 2003/early 2004 up-pipe or order a new one from the dealer.
The only other benefit of the full delete is space, but what really are you going to be putting down in under the intake anyway? Nothing!
