It's really nice to see someone put effort in visual overhaul, however the decision to tie those textures to 10th Anniversary Mod is not a good one for several reasons. Main reason, performance, take a look at these screenshots
They show the scene from Wartok Canyons with increased rendering distance, running at 1280x768 resolution with increased FOV (90 + adjustment for 5:3 aspect ratio) and those textures from Hill of Fire overhaul, sized 512x512, using different rendering outputs; 10th Anniversary Mod, native Direct3D 6 (which you get without setting up anything) and dgVoodoo
wrapper. As you can see, the performance with 10th Anniversary Mod is quite abysmal.
PC where these shots were taken has AMD Phenom II X4 920 CPU and NVIDIA GeForce GTX 750 Ti GPU with the latest drivers and is capable of running newer titles at medium - high settings at 1920 x 1008 resolution at decent FPS. Note that the resolution doesn't make any difference with Drakan. Also, Bump Mapping option doesn't work with 10th Anniversary Mod, so it was disabled for 10th Ann screenshot, hence the visual difference with Arokh and water.
Drakan patched with AiO Patch
supports textures with maximum size of 1024 x 1024. It could be bumped to 2048 if needed, though that's probably an overkill.
Now, on to other limitations, Drakan handles all textures as 16-bit, this is the reason for certain artifacts to show up, I think this is the issue you've written about under Texture Filtering. Nobody has figured out how to patch this limitation out of the engine. For the Texture Coordinates / Texture Wrapping problem, this one really obviously shows up with 10th Anniversary Mod. I tried painting simple square with some random rainbow image I found online, and there were strange lines visible at some places where the one polygons's texture meets another. Replacing texture the right way didn't produce said artifact.
About sprite animations, this one is really a no brainer as the Level Editor gives you control over them, but if you use 10th Anniversary Mod's hacky way of doing things, then good luck figuring out the right order. Same goes for categorization, Drakan has textures neatly organized in specialized texture databases, you can find them under Drakan directory by .txd extension. They're opened in the editor along with the level you're working on. Usually, a group of levels shares a common texture database and each level can also have its own texture database with textures specific to said level. Textures in each database are usually logically ordered by what kind of terrain they cover etc.
As for the skybox, it's possible to change Follow Mode property of sky object to Hold Position, that makes it show a little differently. But yeah, skybox is essentially a special model. I don't think you can change how it behaves beyond what is exposed through the editor without the game source code, maybe if you're a really clever hacker you could stuff the right calls in the code to make it do what you want.
I'd suggest you get acquainted with the editing tools and don't forget about AiO Patch
as it includes all community-made enhancements for the game and the tools. I suppose you could still mess with 10th Anniversary Mod's shaders afterward, but given its current buggy state, I don't think it's feasible. Importing the textures with level editor is certainly the way to go. You also get more optimal memory consumption and better loading times. I've written about the issues with 10th Anniversary Mod several times already, everything from visual glitches, inability to alt-tab out of fullscreen mode without the game breaking, the installer "englishifying" non-english versions of the game. Also, switching resolutions and from fullscreen->windowed mode and vice-versa doesn't work, neither do savegame snapshots and game screenshot feature, though the latter one is also broken in a different way on recent NVIDIA drivers or when running the game through dgVoodoo.