Most after-market WI kits are added as a simple safety measure, ie enabled for trackdays, spirited drives and enabled above a desired boost pressure, in most cases the fuelling, ignition and boost are unaffected, you can of course map for the WI but you would need safety guards in place to detect a failure in the system or risk losing the engine, all of which is possible of course. They normally consist of single a jet placed on the inlet, there are also various positions depending on which end affect is required, ie charge cooling or octane increase, then there are multiport setups which have a jet per cylinder, these systems would normally be mapped and have the required safety feedback.
Using a flexfuel sensor the ECU handles everything, running more aggressive torque, boost and fueling etc resulting in more torque and power, you have all the safety features included and dont have to worry another system running in parallel possibly failing.