I've been using a Skymap 2 and a KLN94B for 4 years, and have never (once it has picked up enough satellites) seen its displayed altitude to be more than 50ft different from the elevation of a known place on the ground.
Once one gets airborne, the GPS will normally be more accurate, due to simple altimetry errors due to the atmosphere deviating from ISA. At 10,000 ft the altimeter error could easily be 500ft whereas the GPS will still be perhaps 50ft out.
I always check both altimeters against the GPS altitude when doing an IAP in IMC, and if the error was more than about 200ft (which I have never seen, in 350hrs of flying) I would go somewhere with an ILS. There is no point in risking one's life just because a large group of PPLs distrust technology
GTW - the person you spoke to doesn't have a clue. The altitude computation is part of the lat/long computation and is only slightly less accurate because of the angle of the satellites. I don't think he actually writes the software in question - very few people do that bit because most GPS receivers are purchased ready-made from 2 or 3 suppliers.
There are situations where the altitude figure can be wildly out, and these are the same as why the lat/long figures can be wildly out: ancient GPS receiver with buggy software, poor reception due to not using a rooftop aerial in a metal cockpit.
Obviously altimeters are used as the primary reference for good reasons, but that isn't the question we are discussing here.