Issue with OR transparency/bald NPCs

AMD is pretty buggy for OR. The developer (Alenet) doesn't own AMD and has admitted that there are some problems. Your best bet is to find workarounds like you are doing. There are no true fixes. You'll have to sacrifice one thing for the other.

Yeah I still haven't noticed any issues or changes whatsoever with deleting the extra shaders folder but I'm not too much of a realism fan so I might just not be noticing it.

I think extra shaders are for the shadows. But I don't precisely recall. Your call if you don't want shadows, but your best bet for a bug free (as possible. Some thing are buggy) experience is to buy nVidia. I wouldn't do that for one mod, but that's me.

So, according to the shader logs, the only shader included in OR and used on the models doing this is SLS2009.pso. I modified the shader to just spit out the base texture and the issue still occurred, but when I deleted the shader altogether, it didn't., so maybe the issue has to do with the way OR redirects the shaders or something, IDK.
Other shaders used by the model: (SLS2008.vso SLS2009.pso), (SLS2036.vso SLS2041.pso), (SLS1S001.vso SLS1030.pso)
I don't know anything about DirectX, so that's all the insight I can give.

I heard Alenet is totally rewriting the shaders. Maybe that will fix the issues with NPCs?

No change in v 9.0.0.

For those who have transparent armours and parts of body in interiors you can delete folder "Interiors" in Oblivion\Data\Shaders\OblivionReloaded\Shaders\Interiors.
I did it and bugs inside of building disappeared and all shadows outside still work. Don't know if it'll cause any errors in future but after playing for a while I did't notice anything

I read it was a compiler thing, and the newest version (9.0.1) fixes the issue. I haven't yet tested, personally.