I'm very confused. What are the possible postdoc options for a PhD in metabolic network reconstruction? Do I need to restrict myself to metabolic network reconstruction? What are the chances of expanding my boundaries? Will a Principal Investigator (PI) choose me for new unrelated topics? Is applying for open positions a good option or write a research proposal and approach for PIs directly, irrespective of position?

It's about what skills you learn that can be applied to many different topics.

If you've completed your PhD, I would have hoped you would have obtained this knowledge already...

But here you go, I will tell you. You need to look on places like jobs.ac.uk (or similar if you are overseas) and find things that look suitable, then look at the essential and desirable requirements. With this, you should be able to tell what postdocs you are suitable for.