Quite honestly you setup with Sketchup running in Wine but Indigo running natively in Linux sounds pretty inefficient for a reason you already provided. You have to mess around with the file locations in the its file manually.
When you get to render more complex scenes, perhaps with external meshes, materials, image maps for diffuse bump, spec ad displacement mapping, UV maps that I could imagine gets to be a real hassle.
If it has to be Sketchup I'd suggest a Windows based system.
If you are willing to learn another very capable 3D software that runs natively in Linux, has an very good exporter then Blender is the way to go. Naturally that would totally eliminate the need to manually edit the igs file.
As much as I am a Blender fan, however, and as much as I love my OSX environment, Sketchup has some very nifty modeling tools that make it very efficient for certain tasks, that you won't have in Blender. Also Sketchup runs much smoother on a Windows system than in OSX.
Just some food for thought
