Welcome to the far future
I've heard a few ideas for the whys and hows, mostly setting laws and such. My take is a little different.
I too soon realized when HG (the CT version) came out ages ago with its onboard fuel purifiers that nobody would build a ship without them or ever buy refined fuel again. The cost breakpoint for a merchant came out just short of even for the basic Free Trader factoring loss of revenue cargo space iirc. And anything bigger or with longer legs was saving money. And with misjumps nobody would use unrefined if onboard purifiers were as small and cheap as they were.
Rather than mess with changing the prices I reinvented the fuel definitions based on the loose terminology as an excuse.
Originally there was unrefined (causing problems but free for skimming or only available at poorer ports for Cr100/ton) and refined (no problems and only available at better ports for Cr500/ton). Then along comes purified (note the minor difference in nomenclature) that is described as refined.
My solution was three fuel qualities:
Unrefined: Free for the taking by skimming or scooping with the proper equipment, but unusable as is. Before it can be used it must be purified.
This is a new definition of the term, and a new fuel type, really a non-fuel type.
Purified: By employing small, basic, cheap purifiers unrefined fuel can be easily and quickly made serviceable for drives though at some risk of contamination of the drives leading to breakdowns or misjumps. Shipboard purifiers are common on almost all ships as a backup but not to be relied on for routine use. Purified fuel is also routinely available at smaller backwater starports (C and D) for Cr100/ton where better facilities don't exist or demand can't support them.
This is the old unrefined fuel, with a new name and explanation, that incorporates the onboard fuel purifier rules.
Refined: Only possible with large and expensive installations and requiring considerable time purified fuel can be further processed until it is refined to the point of being pure enough to reliably perform without complications. Only better quality starports (A and B) can afford the infrastructure to produce this level of fuel and it sells for a premium price, Cr500/ton, but is worth it for the safe operation and long life of the expensive drives. Some large ships may include such aboard but it is rare except for military ships due to the expense, volume and time required to refine. Smaller military ships routinely use purified fuel under strict practices to reduce the chance of drive malfunction.
This is of course the old Refined fuel given a new reasoning and not being permitted as a small or cheap onboard option.
It works for me