I read the page you linked and searched Google to see if the application segments should be written in a particular order but I could not find any evidence for that. The code of ImageMagick 'for eaches' the profile lists and writes them to the file. They are internally stored in a splay tree (https://en.wikipedia.org/wiki/Splay_tree) so I don't think the order can be forced.
Why don't you use Magick.NET to remove some of the application markers?
Why don't you use Magick.NET to remove some of the application markers?