This seems like simultaneous data and address scrambling. I would have to know what game's graphics are there at offset 0 to have any hint at how to deduce the bit order.
If it helps, here is the best approximation I could get of addresses 10-400F and 100010-10400F (which are comprised of Nice Code games):
10 = unknown CHR bank w/ large font; does not appear to be a game, possibly multicart menu CHR
1010 = Spider-Man (Nice Code) CHR bank 1
2010 = blank, likely tied to unknown CHR bank
3010 = Spider Man (Nice Code) CHR bank 2
100010 = Garden War/Resistant CHR bank 1
101010 = Gate CHR bank 1
102010 = Garden War/Resistant CHR bank 2
103010 = Gate CHR bank 2
Note that Garden War and Resistant (as its unaltered ROM) share the same file as each other, so I can't say which one it is off of CHR alone. The following byte areas are swapped around (while still under 4BPP display for the 319-in-1, x16 display mode for the unaltered NES ROMs):
code lines [xx]20-3F and [xx]40-5F are swapped with each other
code lines [xx]A0-BF and [xx]C0-DF are swapped with each other