I have my Apple TV set tp custom, not auto sync and the box below is not checked. This way I don't sync any movies, tv shows, or music, just photos. Then I can go in to the my _____ whatever section of movies, tv, music on my Apple TV and stream any movie, tv show, or music as long as iTunes is running on my computer.
I too have iPhone versions of some of my movies but just a few. If you uncheck the box next to the movie, tv show, or music name in iTunes, it does not appear in the list when streaming. I simply choose then to sync the iPhone movies I want to to my phone but not have them checked and they don't appear on my TV/Apple TV menus. Also, I right click on the movie titles in iTunes and go to the sorting tab and put under sorting name the name of the iPhone version of the movie with 999 in front of it + a space, as in 999 Fight Club i. I name all my iPhone rips with i at the end telling me it is the iPhone version. Also by putting the 999 or you can use a letter z in front of the title for sorting, all my iPhone versions end up at the end of the list grouped together. The reason I use 999 and not z is that I have 50 first dates in my regular movies and for some reason it puts #s at the end, so using the z method put all the iPhone movies before it. Using 999 put them after.