Please consider evaluating if gpios on the io extender should have wake-up capability,
I doubt this is correct, i2c1 should operate on 2.2MHz, at it is used to control twl4030 regulators (SmartReflex that is).
Also, IR diode on N900 is not driven by a simple gpio, but through PWM output. If TX diode on Neo900 is going to use the same, then it cannot be attached to iox.
In addition, twl4030 have 18 GPIOs, are all of them used?