One question pretty much in general about bacterial fermentation and I'll use acetic acid as and example. Originally almost all of the acetic acid (vinegar) was produced via bacterial fermentation but now this is only used for food vinegar. Acetic Acid for industrial use is produced via direct chemical synthesis and it on of the big petrochemical products.
I was unable to find its total production but its one of the basic chemicals we synthesis.
The point is if after all these years fermentation is not a competitive synthesis route for acetic acid except where mandated by law why would any fermentation process be expected to produce fuel at reasonable cost ?

We can't even do it today for industrial chemicals much less for fuel.

I just think we have a fundamental problem here. I'm not saying we can't do this in the future for fuels where we can't substitute but given the above I just don't see how it could ever be a replacement for today's fuel usage patterns.

In general most of the chemical we make also have alternative "natural" routes that have been used in the past. However its rare to see a natural product competitive in the bulk chemical market place and these are high value usages not fuel.