"As I stated above, I have the Indie License which means I should be able to export meshes at 4096x4096 resolution but no matter which resolution I pick, I receive a warning that I am exceeding the 4096x4096 limit for my license and that my output will contain watermarks."
I still get the error above as well, but meshes and other files do build properly and without a watermark. Support did say that issue was going to be looked at and resolved.
Cant comment on your CPU usage. This version of Gaea has been the lightest and fastest of all the releases for me. Have you run and sent Watson logs to Gaea Support?