Fuel purifier has a minimum size. Canon Scout/Courier has 3 dTons available cargo space. Only purifier small enough to be retrofitted to a Book-2 scout is a TL15 model. Of course, if you build a scout using HG-II components, there's plenty of room.
And if using LBB2 rules, I don't remember purifiers being there.
Modifiers for missjump and drive failure (pg 6) are +1 if using unrefined fuel and not equiped to do so, and is told that military and quasi military ships use unrefined fuel because their drives are specialy built to use it, but I cannot find any reference to purifiers....
And, as you say, if using HG2 rules, the lower fuel needs for the PP allow it to mount a purifier...