Thanks for the information about the topic. I hadn’t seen it – it’s a very interesting question.
Warning: what comes next is my personal opinion, and not that of an IELTS examiner or the IELTS organization or even an IELTS teacher!
I don’t think you should worry about choosing between the two layouts that you describe.
Let me explain, using Task 1 in the General Training (not Academic) as an example. In Task 1 in General Training you have bullet points and you MUST deal with each of these. It's the same in Task 1 in the Academic module: you MUST cover all the features of the graph or chart.
However in the example question you have given, or indeed in most Task 2 questions, I don’t think there is a real requirement to discuss each or even any subtopics. If this is an IELTS topic, I think the examiners are adding these subpoints with the aim of giving you some help.
If they had written:
Food has become cheaper and food production has increased over the last few decades. However, some believe this will do harm to the health of humans and local community as a whole.
…many people would not have known why food production has increased or why food has become cheaper. It would be a tough topic for many people - they would have no idea where to start.
However, by writing...
Food has become cheaper and food production has increased thanks to enlarged manufacturing capacity, the use of fertilizer and better machinery. However, some believe this will do harm to the health of humans and local community as a whole. To what extent do you agree or disagree?
...they are giving some suggestions to candidates who might not know where to start.
I think here perhaps IELTS were trying to help by giving more information and ideas to start you off. However, in my opinion, you don’t have to deal with each of the subtopics (fertilizer,machinery, enlarged manufacturing capacity).
There are hundreds of other reasons for increased output in agriculture: farm consolidation, new breeds of food plants and animals, new weedkillers, new pesticides, improved food storage, better medical treatment for animals, genetic engineering, improved communications which allow food to travel more quickly, better irrigation, better training of farmers, better national agricultural policies, freer trade between nations, specialization, and a host of political, economic and technological factors. You could pick some of these.
As far as I can see, the three sub-headings are there to help candidates who would otherwise not have a clue.
However, if you organized your essay as you say (3773, with the first body paragraph about the benefits and the second about the potential problems), that would be absolutely fine. There is no need to write about the benefits or disadvantages of fertilizer or the plusses and minuses of better machinery.
However, I would be interested to hear what IELTS teachers say about this. Any opinions? If you know a friendly IELTS teacher, or even a friendly IELTS examiner (not many of them around), ask them to contribute here!
On a side note, a lot of research shows that the longer the topic and the more information it gives, the worse the essays that students write. IELTS generally tries to keep topics short and tests extensively. Did anyone else see this topic?