Known unknowns...
"The problem is that no one has ever done a comprehensive study of how good the filters on altimeters are, so no one knows how bad the problem will be."
Better get on with doing a study then rather than speculating what may or may not happen. We can speculate 'til the cows come home and I am sure there are good arguments for both sides.
The reality (and outcome of a thorough study) will probably be somewhere in the middle of the two extremes, resulting in a qualified 'go ahead, but within the following parameters'.