Bio? Bring it on! I've been running Bio/ Bio blend since 2004. As long as the fuel is kept clean it burns great and keeps the DPF cleaner. Also provides a better lube for the fuel system than reg Dino Diesel. Can you get a bad batch sure. I had a huge alge/ bacteria issue on a ship I work on when we were in dry dock last spring. temps inside the drydock got over 85 and the bugs just took over the bottom of our fuel tank. The fuel would not flow through a window screen. That fuel was not Bio. Our supplier had said the fuel was treated with anti fungus stuff but as we learned it was not. Keep on top of your fuel, Keep water out, treat it if you have a storage tank and you'll never have an issue.
Depends on the % and the DPF system. Newer systems with a dedicated exhaust injector don't suffer. Bio injected on the exhaust stroke on older cheap systems w/o a dedicated injector doesn't evaporate well and hits the cylinder walls. So does some #2, but, #2 evaporates back out of the engine oil. Biodiesel does not. So higher concentrations lead to the inability to evaporate enough fuel to burn the DPF clean on regen and contaminate the engine oil. Can be bad enough to thin the engine oil down a grade a loose oil pressure hot. UOA won't see biodiesel as "fuel". Not even with the crankcase has risen 3-4 quarts from Bio DPF cleaning attempts. No, not injector failure, 2008 DPF post injection cleaning attempts on B99 and factory oil change at 10,000 miles. Never made 10,000 miles due to low oil pressure alarms. Some of the old DPF systems had oil contamination issues on just #2 diesel.
Bio has less BTU and will reduce your MPG by up to 10%. You need to change your oil more often.
Odds are pretty good you will find bad fuel somewhere in the USA. If not maybe store the fuel too long. Water in tanks is a given. As you noted your supplier didn't treat the fuel or the bugs became immune to the treatment. Bio just makes the bug problem worse as ULSD holds more water is more prone to bugs than the old diesel. Even old diesel could get hit with bugs.
All you can do is protect yourself from this new fuel. Better dedicated water separator as this is what Cummins suggests for up to 20% biodiesel. In cold weather biodiesel has a low cloud point you will have to look into by %. Hot weather brings on better conditions for bugs.
Old metal tank linings are not compatible and can flake/peal off, lift pumps are not compatible, hoses swell up and fail...

One has to be careful with it and take steps to deal with the "Happy Joy Joy" states approving attempting to use this stuff on fuel systems that were not designed for it let alone in concentrations higher than recommended. Again water separator, inspect fuel hoses often, and look into using dual phase Biocide. The cost of this going south is your injection system and a bad injection system can take out the complete engine. I have only had to replace the fuel system from the fuel tank to the injector tips.
With all the screwing around with our fuel everyone gets a crick in their neck from "looking the other way" over increased NOx emissions from Biodiesel. You know the big EGR cooler and turbo clogging amounts of EGR used or DEF used to reduce NOx emissions on your newer diesels? VW being targeted by the EPA over NOx emissions. And yet we have Biodiesel, up to B100, EPA and DOT approved as an alternate fuel even though it can cause enough additional NOx emissions to emissions decertify the engine. No tinfoil hat needed here to see the hypocrisy.