If you're rendering the grass with MGE, use the modified meshes. They were modified so that the grass mod would work properly with MGE. If you don't want MGE to render the grass, then there's no need to use them, just use the originals.
Ok, but those modified meshes look alot different? I think we're talking both about different meshes. A few posts back I posted a link to those meshes, could you take a look? I like those meshes alot better then yours, sorry. I think your meshes are too dense, thick and harsh. While those others are alot more subtle and they really blend in with the environment. Here is a comparison screens:
Normal Grass:
http://i190.photobucket.com/albums/z103/journeytoavalon/Morrowind2009-06-2310-54-43-74.jpg
Updated Mesh Grass:
http://i190.photobucket.com/albums/z103/journeytoavalon/Morrowind2009-06-2310-59-33-35.jpg
I like the last one alot more, but it has collision. I almost figured out how to do this with the NiExtraStringData command but I couldn't get it right, please anyone can?