They're probably in local maxima, not in any global maximum, but it's also likely that there is no single global maximum given how different the requirements are for using different energy sources.
The weak bonds is what complex chemistry and thus complex functionality possible. Stronger bonds is dead matter, and dead matter does not compete.
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.
We are art made by microbes. (I like to think.)
ie. It's not an argument against grey goo, it's an argument the grey goo catastrophe rules everywhere and has done so for eons.