Ok what I can gather from this is that this is how this would work for the end user:
1. Go to DS profile to activate Gateway mode.
2. Backup NAND. Gateway then essentially creates a virtual drive of sorts and fools the console into booting it.
3. Once booted from "emulated NAND" you can update to 6.3. The update just gets installed into the emulated NAND instead of real NAND. I assume that when/if they figure out an exploit for a newer update, they will then provide a method of installing the emulated NAND in to the real one. But for now they won't provide that feature since obvoisely doing so would prevent you from ever using Gateway again.
4. I have to assume that once you have your emulated NAND updated to 6.3, you CAN NOT boot roms while running from emulated NAND since it has 6.3 which is not exploited yet. Since (currently) the emulated NAND is running a legit firmware (as evidence by the fact that eShop works), any game booted from emulated NAND WILL have online support. Whether or not online support will work when running on real NAND is the question.
5. To play roms again you reboot 3DS to get it to boot real NAND again which was still at 4.5. Then repeat Gateway exploit and this time go to run a rom instead.
6. To return to emulated NAND you just reboot and repeat Gateway exploit and just tell it to boot emulated NAND and then your back to 6.3 where you can (currently) only run legit copies of games.
I think at this point the "spoofing"code is simply updated to redirect the game's firmware check requests to the emulated NAND. But you DO NOT boot that emulated NAND to play said rom! You would have to stay on 4.5. The spoofing is only altered to instead have the game use the emulated NAND once that game is running. That's what I have gathered from how this should work.
Honestly at this point this would be good workaround if v5+ support never comes. At least then you can still use 6.3 and newer firmwares to play stuff you bought from eShop and take advantage of new features in new firmwares while still being able to return to 4.5 when ever one wants to run roms. The only downside that you must have never updated past 4.5 to start out with.
The easiest solution now is to resale a v5+ console and buy one with 4.5 or older firmware on it. You would still have to spend a bit of money to do this. But since your plumping down 80 bucks for a flashcart, this shouldn't be too unreasonable.
Assuming you never update beyond 4.5, this would make Gateway roughly 90% future proof. I don't know the coding details on how the NAND emulation works, but I would bet it would be difficult for the OS/software running in emulated NAND to detect that. It will likely take Nintendo quite awhile to figure out how it was done and how to detect it and even then this only prevents running future firmwares in their emulated NAND. Gateway could then just update their NAND emulation code to get around any future AP measures they put in place.