Colleges that use The College Board’s CSS Profile and use The College Board NPC template are more likely to have accurate NPC results.
However, colleges that use The College Board’s CSS Profile but use a less detailed NPC template (like the Department of Education one) are likely to have less accurate NPC results if the financial situation is not simple (married parents, mainly W-2 income, ordinary assets). But this does not necessarily mean that a reverse-engineered NPC from College Aid Pro will be more accurate – that depends on whether it has a large enough sample size from those with similar financial situations as you for that college.