I am not familiar with the inner depths of spotlight, but I don't think it indexes the
Userhome/Library/Application Support
folder, where our autosave folder and other temporary information is stored. We never really had any issues with Spotlight since it was introduced in 10.4 Tiger. We did, however had issues in the past with other applications that scrutinize files, like Norton Antivirus for Mac.
Gergely Kmethy
VP, Customer Success, Graphisoft