Correct. That's how the nxdumptool placed everything. I put my mods in the data folder in A000 along with the vanilla ini files in romfs, and my ccc file with my esp names added is in B009.Ok. Did you see that, now that you have the Anniversary UPGRADE, the ccc file that should contain your mod list IS:
SD:atmosphere\contents\01000A10041EB009\romfs\skyrim_aoc.ccc
and NOT:
SD:atmosphere\contents\01000A10041EA000\romfs\Data\skyrim.ccc
If I even make it to the main menu I haven't gotten any mod warnings when starting a new game