I convert all my sets like this to boxsets and have never had a problem getting the child profiles approved (Cinema Paradiso, The Sand Pebbles, In Old Chicago, etc.).  In addition to the reasons already mentioned for doing so, I like have the ability to track when I watch the alternate version of the movie.  I can also rate them serarately if I choose to (although I don't use the ratings features of the program).  For example I can tell I watched The Sand Pebbles on 11/21 and watched the Roadshow version on 1/26.  And if I used the ratings feature, the Roadshow version would have a much lower Video score.

The great thing about this system is those who want the extra profile can get them and everyone else can ignore them.