The reasoning is fairly obvious - they dont want to see dumb missiles getting upgraded to a DIY guided ballistic missile thanks to a $100 Garmin gaffa taped to the side and a cheap flight control computer.
The intention was for a GPS device to disable itself if it was traveling faster than 1k knots AND above 60k feet, not traveling faster than 1k knots OR above 60k feet. Unfortunately, many GPS devices improperly implement this as an OR condition, rather than an AND condition. This becomes problematic when using a GPS in a high-altitude weather balloon to determine altitude and location, which a few friends and I did a couple years ago. We had to be very careful when selecting the GPS we used to avoid this pitfall.
We used a UBlox5, which we purchased from diydrones.com. This was in 2009, so that particular model is now outdated. Both Adafruit and SparkFun now sell devices which are explicitly listed as being HAB-friendly. There's also good guide at http://showcase.netins.net/web/wallio/GPSrcvrsvs60kft.htm. That page states that SiRF-I and II are known to fail above 60k feet, and that some SiRF-III-based receives fail, while others don't.
(If you happen to be in the Bay Area, I'd be happy to meet up and give you guys some pointers sometime; drop me a private email.)
The receivers use other satellites. They have to anyway: You can't get a fix with only one satellite.
In practice there are enough satellites that these considerations are theoretical. Most situations that would involve limited satellites also introduce stuff like multi path reflections that further degrade position accuracy.
If the machinery experiences significant acceleration in an earthquake, it's not necessarily intact or safe to operate afterwards. The enclosing machine shop is also not likely to be in any state to continue operations if something as large as the pictured CNC machine has been thrown across the room. I don't buy that this issue is a big deal either.
From a software freedom standpoint, yes, this is terrible. But I don't think it's as much of a problem for the owner as the parent suggests.
If the lockdown mechanism is GPS, then it should be clear where the actual machine is, so there shouldn't be any need to lock it down unless it's in a black zone.
And what happens if the manufacturer goes belly-up?