NB that there are bio-diesel fuels that are excellent and add lubricity, some that are bad and some that are atrocious.
The problem is that they’re all called “bio-diesel” when in reality, some of them are utter crap. But let’s put that aside for a sec.
The lubricity in mineral diesel used to be, in large part, due to the sulphur content in the fuel. Now that we have ULSD diesel, we see older diesel fuel systems failing at an appalling rate.
On farm equipment, the situation that worries me the most with ULSD is any engine with an old, rotary Roosa-Master injection pump. They had no crank oil put into them for lubrication, they depending upon the fuel entirely. I’ve got at least two of these types of fuel racks on the farm (in older New Holland equipment, on Perkins or Ford engines) and I have to add fuel conditioner to make sure there’s enough lubrication in the fuel to insure these pumps survive. Losing the pump is a $1000+ proposition every time it happens. I’ve heard of guys losing two in a row before they took the time to ask their fuel jobber “Hey, what’s changed about my fuel?!”
I believe you are mistaken here, bio-diesel is better for the engine as long as you don't have any natural rubber seals. The varnish will not build up or cause problems unless you are running stright vegetable oil instead of bio-diesel.