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.

Acetic acid is made from methanol via the Monsanto or Cativa process. In turn, methanol is made via steam reformation from natural gas.

I'm not disagreeing with anything you said, but this economic advantage is underpinned by large quantities of clean, high EROEI feedstock.

This little discussion illustrates the problem with peak oil. Oil is really cheap in relation to non-oil feed stocks for almost any industrial process. When oil runs out, almost everything will be a lot more expensive. Some things will be more expensive than others and the overall differences will be small compared to what the price had been when oil was available. A big problem is to figure out now what will be cheapest then, in the future, using economic data from now, when the cost of everything is massively distorted by the availability of oil. We need to know what will be cheapest then because we will have very little time to do the development work when we start falling off the cliff.