Yes, if the cover or media is different, it can get its own entry. As stated, if those games inside of that box have "Part of a Set" on them, then each would be titled GameTitle (Part of a Set).
For one of the above examples, would the correct title be '
Hitman: Blood Money (Part of a Set)' or '
Hitman: Blood Money (Part of Hitman Trilogy)'? Though the occurrence would be rare, the latter version would distinguish the set when the game in included in multiple different sets. In that example I used the database title for the set, though that could be an issue with longer set titles. That release of Guitar Hero III was included in the '
Guitar Hero III: Legends of Rock - New Wireless Guitar [NA]' bundle. In situations like that, it may be more apt to abridge the set title (i.e. '
(Part of Wireless Guitar bundle) ), but I would like an official stance on that before making any submissions.