Re: Control electronics
Certainly, barometric, GPS and accelerometer instruments are not mutually exclusive but that isn't really the issue here. Neither GPS nor accelerometers on their own would provide a working solution because accelerometers can't give you location and GPS can't give you attitude rates; they comprise two halves of a single system that need to integrated to produce a working solution.
Sure, you could also carry a barometer but integrating that into the autopilot/FCS not only increases weight but also complexity (in addition to the complexity overhead of integrating the baro data you'll also have to arbitrate between that data and the GPS data when they inevitably disagree).
I'm not sure what you mean by "inertial measurement" here; the accelerometers will be providing inertial data but Vulture 2 isn't going to be carrying a relatively massive inertial reference platform, which you'd need for inertial navigation. In any case, there's the GPS for that (yes, it may not work above 59k ft but that still leaves you those 59k ft to glide back to the landing area once Vulture 2 has descended to that altitude, which should be enough)
I don't think that ram ports built into the airframe will work. I believe that the reason they're on tubes is because they need to take readings from outside the boundary layer whereas sticking them in the nose or the leading edge of the wing, which is where you get the greatest accelerations of air around the airframe, would produce some wildly skewed readings. Having multiple sensors is no guarantee against icing failure either because the conditions that cause one sensor to ice up will apply to all the others too.
I can't see why you would want to switch between flight control and navigation systems in such a relatively simple vehicle just because you're nearer to the ground; it would be as effective as forming a coalition government from two fundamentally different ideologies.
A conventional pitot tube works by ram air pressure, which is combined with static pressure to derive IAS and establishing static pressure in itself is not simply a question of making a hole in the side of the airframe and sticking a sensor in there; the boundary layer airflow across the opening of the hole results in a venturi type effect so the static pressure needs to be calibrated along with the ram pressure. Would not a reversed "negative energy" pitot tube just give you a variation on static pressure? Also, would it guarantee that you get no icing? I've not heard of such a device and unless they already exist in a suitably small, light weight, low power and inexpensive package then I suspect that devising one, and then calibrating it across the environmental envelope of Vulture 2, is going to be a bit beyond the scope of the project.