Why does the Canon S90 focus less closely than the Canon G11 in macro mode?

The main reason is the lens, not the sensor. Although the S90 and G11 share the same sensor, they use different lens designs, and lens design determines how close a camera can focus.

The S90’s lens is designed to be more compact and brighter, which helps keep the camera small and lets in more light, but that comes with tradeoffs. One of those tradeoffs is reduced close-focus ability. The G11 has a larger, slower lens design that allows it to focus much closer.

This is normal in photography: lenses optimized for close focusing often end up larger and/or slower than similar non-macro designs. Sensor size can influence how easy it is to design close-focusing lenses, but between these two cameras, the key difference is that their lenses were optimized for different goals.