If it is formatted with the SD card out, then even if you put it back in, it will create a new folder in sdmc:/Nintendo 3DS/ with a new unique ID.
Actually if you have a <9.2 system, it might still be possible to do some experimenting by getting a legit .cia
I wonder... if you system format, does the 3DS create its new folder in sdmc:/Nintendo 3DS/ only after you finish the initial set up? Or does it create one right away.
Because then someone could possibly start it up, power off, take the SD card out, move the contents of the old Nintendo 3DS folder into the new one that was just created, and see if it will start up and the game will show up on home menu after the initial setup. Pre-installed content is tied to the console itself so it should be properly signed and have the proper tickets regardless.
I could try it on my own, but it would be a hassle because I have my XL all set up on 9.2 with my rxTools, it would be a pain to backup stuff on SD card, format sysnand, have to reinstall menuhax, all that stuff, meh. I mean I guess I could try. I already have all the US legit .cias installed to sysnand so it wouldn't be too difficult for me to try.
Edit: Okay, I just tried it, it doesn't make the folder in sdmc:/Nintendo 3DS/ until after the initial setup, so I don't think there's a way to have pre-installed games show up on the home menu after the initial setup unless it came straight from Nintendo on 9.9
Now I need to re-install those games on sysnand which will be a pain because of how long it takes, but it was worth it to try that out. Needed to know for sure.