[DagAgren]

If using stronger chemical bonds was advantageous, bacteria probably would be doing it already.

The weak bonds is what complex chemistry and thus complex functionality possible. Stronger bonds is dead matter, and dead matter does not compete.

[philipkglass]

Incorporating fluorine in a molecule offers additional flexibility over the more common chlorine and bromine compounds commonly found in natural products. For example, the fluoroquinolone antibiotics are distinguished by their introduction of fluorine, yielding compounds more effective than found in nature.

There are a few fluorinated natural products made by wild organisms, but they are very rare considering the elemental abundance of fluorine on Earth and the high utility found for fluorine in pharmaceutical development:

https://www.ncbi.nlm.nih.gov/pubmed/23034231

The strong bonds formed by fluorine, and its formation of insoluble compounds with alkaline earth metals, probably explains the rarity of natural fluorinated products. The fluorinated natural products are no more "dead matter" than other poisons evolved by plants against herbivores, but it's hard to evolve out of local minima that exclude fluorinated compounds.