It's not the 1800's any more. We have computers and stuff, we don't have to rely on techniques developed for a time when your navigational tools consisted of a map, a compass and a sextant.
Note: The actual deviation from a great circle route is generally fairly minimal in practice.
PS: GPS is just another system that really can fail.
a Mercator projection will give you a bearing to steer to arrive at your destination, which can be followed by eye, autopilot, etc etc.
Calculating a great circle arc and plotting it, following a bearing which may only change by a degree or two but isn't constant, is an unnecessary complication on short routes.
Even commercial vessels will use those old techniques if they don't need to consider the longer range effects. Error correction in the human process is always a consideration.
(Not even talking about data entry errors in GPS systems, but that Malaysia - Melbourne story was Funny.)