The reason is, as indicated, simply because hunt & ass don't share the same race.
knowing that, the fact to work with .mlx files or with the .mlt files doesn't make any diff (except than the first can reduce your workload by 4).
in both cases, the base filename defines the final class which use the models ('de?f' means deatheater + fighter and thus is relevant for warrior & guardian, 'de?r' means deatheater + ranger and thus means hunter).
I'm pretty sure you know that, and you edited your mlx (or mlt) files finely, but still some sets (at last the rabbit costum) is not defined with the same index in the de?r & vi?r files (again, mlx or mlt).
once the models are created or edited, we edit gears with the Light or Dark Gears Editor (if using shStudio), there some models are displayed but the information is not comprehensive and this can introduce errors (and I think more errors than the use of mlx instead of mlx).
what is the issue there?
a gear item is not intrinsiquely dedicated to a specific class, instead we choose which faction can use it and then which classes can used it (from 0 to the 6 available).
when it tries to display the 3D view of a gear, the editor can not rely on a constant / reliable information to know from which mlt files the given model must be read, this is determined by the selected classes. it's fine for a gear used similar classes (warrior & guardian for instance), but when the gear is used by 2+ classes belonging to 2 races, there is an issue.
in this particular case, when editing a top protector usable by both hunters and assassins, is that model must be read from DeathEater/demr_upper.mlt or from Vile/vimr_upper.mlt?
the only certainty is that it can not be read from the two files at once.
in such a case the model displayed by shStudio is the assassin one (so the one defined in vimr.mlt), if you want double-check the appearance of the gear when worn by a hunter, you must uncheck the 'assassin' box, keep the 'hunter' box checked (if this one only), validate & re-open the dialog. the data of the gear item will be unchanged (of course), the index of the model will the be same (since it's an item data) but the displayed gear is not the same, because another mlt file is read and it (very likely) does not contain the same 3DC & DDS filenames.
in short: an item defines an index of model but it doesn't define the file in which this index must be used; only the class using the item (so in-game) defines the model file to be used.