I don't want to go running my mouth until we get hands on the actual code as I'm not sure that the decompiled dlls represen the actual input code. But as far as the structure goes so far yeah it seems a bit haphazard. There seems to be multiple implementations for the same features here and there, which is indicative of a communication bteakdown in the dev team, or attrition and iteration without a proper cleanup process.
I'm assuming that this is just part of EA, the cleanup passes are simply yet to be done and TW is still experimenting with the best ways to structure the code. I think this is why they have been saying that the modding tools will be released much closer to the actual release date - most of these systems will change and any mods we make today will likely be broken in a couple months.
But hey we're modders. No documentation, no comments, no support? No worries.