Good question. I'd like to know other peoples' experiences with problems similar in Milkshape.
Currently, I'm trying using Milkshape to make levels for a 3D overhead shooter. Getting textures positioned just the way you want them is a pain in the neck, but I think I'm getting the hang of it. However, I'm segmenting my scrolling levels in screen sizes for both memory and ease of texturing.
If you ask me, go for it, as long as you feel you've got a really good grasp on the texturing issues.
"Power, precision, and don't forget about speed. If you practice everyday with these things in mind... you begin to develope A FIGHTING MODE." - Fist of Legend (Jet Li)