Let me see if I understand what you're attempting ...
You have a 1.6l, 16v engine with no distributor, and you want to run it with a Megasquirt - you don't want to use the crank sensor, and you don't want to buy a distributor.
I've never used a Megasquirt - but - it doesn't matter what engine management system you choose, it MUST have some sort of timing reference - either some sort of crank position sensing - or some sort of cam position sensing.
I don't understand your reluctance to buy a distributor, but, lets assume you plan on running a distributorless igntion system - either two coils in a wasted spark configuration (which by the way Suzuki did use on the later versions of the 1.6l, 16v engine) or quad coils - you're going to need a sensor either on the crank or on the cam to tell it which coil to fire when.
Let's go the other way - you're going to run a distributor to handle the ignition - and lets assume you can find one completely self contained with no connection to the ECU. You still need a sensor on either the crank or the cam to tell the ECU at a minimum, how fast the engine is turning because that determinesthe when or how often fuel gets injected - if you run batch fire injection - or if you're going to run sequential injection, it also determines the where or which injector to fire.
Are you getting the point here? Your ECU MUST have a timing input from either the crank or the cam - the easiest way is probably to get it off the distributor which is how Suzuki does it. You don't HAVE to do it that way, but if you don't, then you're going to need another sensor somewhere - the advantage of an aftermarket ECU is that you have a wider range of choices as to how to do the sensing - but it still has to be done.
Oh - to answer your question - the 96 setup is not "independent from any computer" - it is an input to the computer, and since the computer controls the igntion advance and determines when the plugs are fired, in a way, it's also an output from the computer.