This is kinda an important quote from that link: "No two cars were assembled exactly the same. In fact, the same car is not the same from one side to the other. Everything wasn’t intended to be perfect, it just had to be within an acceptable tolerance. Now if you add thirty or so years of usage and maybe even a bump or two, you can see why no car is going to be perfectly “square.” Learn it, live it, love it or else you'll be tearing out your hair LOL!
1. In the link, their holes were above, below and in the cut line. As long as the hole isn't full of jagged metal it will weld up just fine.
2. You may need to apply paint with either a spray wand extension (long hose) or an artists brush taped to a stick. A shortened brush taped to a pipe cleaner will get you the articulation you need.
3. Once you get the hang of using a cutting wheel it's easy to adjust the depth of your plunge cut. Don't worry if you cut though the trunk pan, just weld it back up.
4. Parts of it should end up in the trunk and some between the inner and out panel. You may need to make some preliminary cuts to make things a little easier.
On the last thing, I would try to avoid the lock cage area all together. Just cut across the filler tube opening. See why SOMETIMES it's easier to change out the whole panel?

This only looks difficult.
Think on this while you are sick, but don't do it until you are well. Last spring I got pneumonia, the Docs blamed my younger sister who had strep throat. I think all the welding fumes and grinding I was doing at the time mixed with me having the flu and the little one giving me strep caused my pneumonia. Better safe than sorry!