Let me try to answer a few Q:s.
1) Ripping: AnyDVD HD presents the BD to the OS in an unencrypted form. The means MC can play and rip this encrypted content just fine. Also once ripped it is no longer encrypted and will play just fine without AnyDVD HD and the directory can be copied to other PC if you want. If you use AnyDVD HD's rip to protected ISO then to play it back in MC, you will need to first mount the ISO, and like a physical disc, AnyDVD HD needs to do it's magic before MC can play it.
2) Streams: Most of the Video/Audio streams are actually muxed inside the m2ts files itself. So with a prog like makeMKV shows you these streams and gives you the option to create a NEW BD with only the streams you want. If you like, these are Remuxing (Re authoring Tools) and is (currently) outside the scope of what MC or AnyDVD HD does. MC will let you choose which of these streams that should be used during playback. Alternatively some discs also keep content in separate m2ts files (eg extras, etc). If you don't what these ones you can delete them but they tend to be small and if you don't know what you are doing you could break you playback of the Main item.
