Are you saying that the last track in Playing Now is faded out (or cut short) when playback stops and when you add new files to Playing Now and play them you will first hear the missing tail of the last played track? (I can't reproduce this.)
If you mean that you would like disable cross-fading only between certain tracks depending on their position in certain playlists, I don't see how that could be possible.
(Edit: You probably already know the following, but it might be useful for others.)
Inside MC the playlists are either static listings or rule based filtered views of the database files. When a playlist is played the included files are added to the Playing Now queue list (the exact behavior depends of which play command was issued, e.g.: play (replaces), add to end, add as next to play, etc.)
MC has no reference of which library view or playlist was used for viewing the tracks at the moment they were sent to Playing Now. The played tracks are cross-faded if cross-fading is enabled, however the last track is not faded out.
