The reason that GPS altitude should not be used is nothing to do with its accuracy. The reason is that everyone else is using barometric altitudes, and all restrictions such as airspace are defined as barometric altitudes.
jxk
200 feet is within the standards for IFR flight in controlled airspace. Don't worry about it, mention it to your maintainers when convenient. Always fly what your altimeter is saying, having checked the correct subscale setting, unless you have a reason to doubt that it works (like my colleagues sudden apparent ascent to 10,000 feet plus due to a mechanical failure within the instrument!).