Many airports are technically not at the correct altitude so when you place a good mesh in the sim those airports that fit the poorly modeled mesh no longer fit a proper mesh. Luckily some of it does fit so the good mesh is still desirable just will have some flaws that will need to be address by you if they bother you.
I ran into a good example of this about a year ago. I purchased USA Waters by R. Tarburet.
USA waters is a detailed update for Rivers - Coastlines - Streams - Lakes for the United States Territories. Covers the whole of the States - other than Puerto Rico. Waters bodies are positioned and designed accordingly to high resolution digital data - to reflect realistic position - shapes and dimensions for the whole of the United States. Offer full compatibility with any Terrain usgs / srtm designed terrain mesh - Manhattan Scenery - Lennart Textures - USA Roads scenery.