The only explanation I can put on altering difficulty is that as a player, you have certain options to make the game harder for yourself. (Don't upgrade the sword, don't upgrade your tunic, don't get any heart pieces, the 3 heart challenge, don't use any bottles, etc...) Although I'm not sure if that's what you meant.
I don't think its fair to almost ever consider a game to be the best above all else. Instead I like to bunch games in tiers, and Ocarina of Time is in the top tier. I would say that it is clearly one of the best games ever made for the Nintendo 64.
I'm just not about to start comparing it to Link to the Past, Super Mario 3, Grand Theft Auto 4, Half-Life 2, Chrono Trigger, etc... Games that are completely different genres and in some cases came out 10 years before hand or 10 years later. It's only fair to compare it to the games of its time and specifically of its console and genre. In that sense, I think of its genre, it is my favorite and thus (I suppose) the best game for the N64. Although I'm sure there would be plenty that would argue Super Mario 64, Conker, Goldeneye, Banjo-Kazooie, etc... Heck many fans here have even said that they prefer Majora's Mask in other threads.