Actually, I've been playing around with a different approach to modding because my file structure was getting all muddled up. vesselData.xml and artemis.ini are using paths off of the root Artemis folder to load assets like models, textures, and (in artemis.ini's case) sounds, so we could have a Mod folder with subdirectories containing all of the files we need for a given mod-- something like Mods/BSG in the Artemis directory, for example-- that contains additional folders for textures, models, and sounds.
Then, you create altered versions of vesselData.xml and artemis.ini (call them, say, vesselData_BSG.xml and artemis_BSG.ini) that reference those assets. For example, in the BSG mod, the Cygnus asset calls would look like this:
<art meshfile="Mods/BSG/models/cygnus.dxs" diffuseFile="Mods/BSG/textures/vidar.png" scale="0.5"/>
<internal_data file="Mods/BSG/models/cygnus.snt" />
Now, all you have to do is worry about copying/renaming vesselData_BSG.xml and artemis_BSG.ini into the correct locations (which a bat file can handle easily) and everything* (*see Primary Drawfack, below) will load up properly without you having to worry about how/what to clean up/copy back afterwards, and your dat directory will remain nice and clean.
The primary drawback is that in the BSG mods's case, the UI elements (which are my favorite parts so far!) will still need to be copied into the dat directory, because there's no way in place yet to have that dictated by an ini-type file. Also, layering mods (Pitting your Glactica model against a Star Destroyer, for instance) would be problematic, but I guess you could probably write a script to compile those combos for you.