Does not affect location. I stayed in the spot where I was when I injected the data.
Basically, it looks like it changed all constant data. Essentially anything not being edited in real time. My location did not change and my play time did not change.
I had my original game, on a Sky3DS Flash card. I used the tool to export that save to my SD card. I then turned off my 3DS, put in a new cartridge of Omega Ruby, and started the game. I got to the point where I was at the first Pokecenter. I did not have a Pokedex, any items, basically anything. Lots of options were disables, no map, you get the idea.
I then minimized the game, used the browser to inject my save data that I had exported from my Sky3DS, then went back into the game. I was still standing in the same location, but my Trainer ID had changed, my money, all Pokemon in the PC, items, what options i had available (like the map and such). Play time did not change, my location did not change, and my party did not change. Other than that it all looked good.
Can not comment on gender, as I started both games as a boy.
How does it not make sense? Follow the steps you see in the first post. But, at step 11 (11. Run X/Y/OR/AS and get in game (make sure you can see Brendan/May).), you would be using a new cartridge. I played the new cartridge until I was at the first Pokecenter and PC so I could verify my PC Pokemon had transferred correctly.