Never read through the GodMode9 sources (not sure where to even start). But it is the only thing that makes sense. Ninfs can't open a backup without the OPT so it must be present in decrypted form within the image (or provided separately).Are you saying that even though the NAND is encrypted, when Godmode9 embeds stuff into the NAND, then that particular embedded data is decrypted? I've never really been clear on that – it seems so strange, because it's a dead giveaway that Godmode9 was run on the 3DS, and hardly anyone is likely to go through the hassle of reading the NAND from a dead 3DS. Or so I would think.
All 2|3DS NAND chips are a bit larger than the sum of the partitions. Some from the "New" series have 4GB if I remember correctly (and can have a nice bonus drive in GodMode9 for storing data). In any case there is unused space that will never get overwritten by the actual OS for storing essentials.exefs.
GodMode9 does nothing to hide its usage. As for the "reading from a dead console": Surely not going to happen often if at all. But since the embedded backup is part of each backup image it comes in handy fairly often. There is more than the OPT stored – the movable.sed for example is also in there. Believe me, this is a really good idea. A good safety net.
This is the reason why we always say: "Stick to 3ds.hacks.guide and nothing else." Those videos caused much trouble in the past and people a) Seem to prefer videos over written guides and b) get directed to videos from search engines.(You could of been more clear in your language Mr. "Jack Sorrel")
What I suspect these video authors are doing is (often badly) copy 3ds.hacks.guide into video form and sometimes providing "convenient all-in-one packages" for "easier" installation which brings a lot of potential trouble in itself. If they are successful with their videos they can even earn money for the work other people have done (CFW developers, 3ds.hacks.guide authors).
Normally not a Google user, I just typed "Install custom firmware on 3DS" into Google search. Unsurprisingly the top results were YouTube(=Google) videos.