No, it's the result you get when people work with real numbers in computers instead of theory on a chalk board. Try computing the cos of Latitude when you're on the equator. That's a very real problem, and if you forget to handle the exception and someone flies your autopilot across the equator and the GPS hits it just right, someone could die.
It'd be much better if the hardware just delt with it, and by naming this thing he justifies changing the hardware.
I do not think that crossing the equator would be any reason for concern. I suspect this has been "worked around" many times and that there are many redundant systems in aircraft to take care of the problem.