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"I'm assuming that's why the surface is being rebuilt from 0,0?"
EDIT: i thought you were referring to the Graphics.DrawTexture call, but you were talking about something else. my bad.
calling Graphics.DrawTexture(new Rect(0, 0, 0, 0), syphonRT) has nothing to do with IOSurface/Syphon/logic/sanity. It is a wonky Unity workaround to basically force GL to clean up its act, so that by the time it serves the texture to Syphon, its matrices are popped. This way, it will be completely done rendering regardless of whatever magic Unity is doing behind the scenes by the time you serve the screen texture.
I found that fix accidently after days/weeks of fighting with Syphon/Unity, and it only still exists because I know not of any other way to make it work.