I think you've answered your own question.
The occupations are free, and you start the next game with them.
The food is a bonus for getting higher than the benchmark.
Because the benchmark keeps rising, there's nothing else to worry about.
Otherwise, the rules would tell you to 'pay' for your additional permenant occupations. They are silent on the matter.

This raises another question: Is the food cost printed on the action space based on the number of occupations that you have in play, or the number of time that you play on that space? In other words, the first time that you play on the "Occupation" space in the second game of the series, do you get that one for free (since it was the first time you played there this game) or do you have to pay one food (since you already have the occupation in play). Sorry, I don't have the board in front of me to check the wording.

My point of view

The rules state that the permanent occupations are placed before the start of each game. The action space description for 1 occupation refer to the first occupation played in a game being free, so the permanent occupations would not count being played before the game.

So the first use of the space in each game is free.

Per this thread (Susanne Rosenberg): http://www.boardgamegeek.com/thread/327057, you do have to pay one food for the first time you take the occupation action if you already have a permanent occupation in place. This is why I asked the initial question in the thread - if the rule is that the initial occupation is free, but subsequent occupations are one food each, how do you handle multiple permanent occupations in terms of food consumption requirements?

The cost of the occupation is determined by the manner in which is is played (this is quite obviously the case if you look at some of the actions available with more players that require 2 food to play an occupation).

The cost "1: free, 2+: 1 food" is not globally applied to occupations, only occupations played via THAT action space. Permanent occupations are not placed via that action space and thus do not have that action space's cost associated with them.

It's also reasonable (and correct) to assume that you only get your first occupation free if you don't already have one. The action space doesn't imply that it's free the first time you use it. In a multiplayer game you could play an occupation for two food, and then go to that action space. It's the first time your using that action space, but it's not your first occupation, so it's not free. The solitaire game is no different. You have to pay because you already have at least one occupation, even though you got it through means other than that particular action space. It doesn't matter where it came from.

Thanks!