Is there a way to set the start position in the manifest to be a negative value?

I have a window that has some extra room on the left and right for tooltips but it’s otherwise transparent. So I would like the starting position to have some of the windows be off-screen. Is this possible? Or is there a better solution?

Nope.
Windows get pushed into the screen if they are opened crossing the edge.
You’ll need to explicitly position it with the overwolf.windows API every time they open.