The highest bit of each 16-bits is always zero. It has a few uses on the DS depending on video mode (transparency bit, LSB of green), but with the camera it's just unused.
Edit: Actually it's probably always one, not zero, I don't remember for sure.
Yeah, that's the major and unfixable issue with this. The 3DS is rather slow at booting apps and this method boots a 3DS mode app which then immediately reboots into DSi mode, at which point it does all the same things NDS forwarder does.
Though it should probably be closer to 5 seconds slower...
The bin simply contains raw 256x192 15bpp BGR bitmap frames concatenated together, with u32 delays in between (in CPU cycles iirc, I meant to make that actually useful with milliseconds or so but haven't gotten around to it)
You probably just need to install Pillow (pip3 install Pillow) to run it.
You could just put pkmn-chest on your flashcard and run it from there instead of the CIA. That said this was actually intended to be supported, I just never got around to actually making it work iirc so I'd totally accept a PR adding it. I just haven't really been working on pkmn-chest for quite...
In the DSi title manager (System -> Manage DSi Titles) it should have an import option that'll let you import .sav or .pub files. I don't have melonDS set up atm so not sure the exact steps, but it should be there.