The "real" Myst Island is substantially larger than the island depicted in the game. Both Cyan and Myst (the game) exist in the Myst universe (in much the same way as Marvel exists in the Marvel universe). In-universe, Cyan simplified Myst Island to make the game both easier to develop and easier to play.
According to Richard Watson, writing from an in-universe perspective:
I want to start by pointing out that Myst/Riven are Cyan's attempt at recreating some of the events in the life of Atrus in a semi-non-linear medium (i.e. a game). Since it's a game where the player can do things that didn't happen in the account of Atrus' life, we've got to take some artistic license with his story - like the "losing" endings of Myst and Riven.
When making the games, we have to carefully pare everything down to the basic elements needed to play the game, leaving out almost anything that isn't required for gameplay. Myst Island, for example was made much smaller, and only the buildings/places relevant to playing Myst were included. Atrus definitely had other "places of protection" for his Books other than the ones shown in Myst. We throw in as many "extras" as we have time for, but for the most part, there isn't much time for things that aren't specifically needed for a playable game.
So the most accurate answer for many of these kinds of issues (e.g. "Why do the remaining Books coincidentally happen to be the Books with 'places of protection'?) is simply "artistic license". If we didn't have hardware limitations, storage capacity limitations, time limitations, money limitations, etc. and if we had a billion monkies [sic] working on a billion computers for a billion years, we could make the Ages more complete, which would be cool from an exploration point of view, but wouldn't make the games themselves any more playable. In fact with all the "non-game related" things thrown in, there would be a lot more "red herrings" and people would be even more confused when they write to me. ☺ (If I had a nickel for everyone who wrote to me asking what one of the few "extra" items in Myst did...)
Watson does not specifically mention farming or other food sources on Myst Island itself, but we can extrapolate the presence of such things, as well as living quarters for Atrus and his family and so on. If these things were not on Myst itself, they must have been on other ages, but either way, they were "deliberately" cut from the game for reasons of scope.