Auditing and enforcement are critical. Shipping around physical gallons does not get rid of that need. Physical gallons could just as easily be water if nobody checks. I don't see why you blame the abstraction.
Or they could never even bother to ship the gallons. That's not a 'scheme' of any sort at the oil company, it's just the business focusing on the part where it makes a profit and dealing with the regulation of buying biodiesel in the most minimal way possible.
It's similar to how we don't see stores abandoning credit cards despite the impressive amount of fraud we see reported on Krebs. Instead the holes get fixed (eventually, with lots of foot-dragging).
The article reports an interesting story but it doesn't seem big enough to have that kind of impact.
Note how in the article the people working there were saying they were 'expecting an audit any day now', but as long as their paycheck depended on not being audited they were all fine with it.
It's rather strange how the CEO is the only person indicted.