Traveller ships deal with cryogenic hydrogen as a matter of routine, so the slower method Aramis describes is probably within reach for most ships. The issue will be speed of adaptability. If a ship needs to change its gas mix in a hurry, having purification systems in the tanks will be vitally important. A slower gas mix change can probably be done by any ship with access to the right feedstock gases and enough patience.
It isn't, in my opinion, that fuel purification systems add much to what a ship can do with the cryogenic fuel (and thus atmospheric feedstock) it carries, but that is alters the ease with which it does those things. Dedicating space to the plumbing of a fuel purification "plant" makes thermal fractionation, gravitational distilling, and easily controllable filtration pump-arounds happen in hours. A ship with "just tanks" can do these things, but much more slowly. The temperature and flow control of the default fuel handling system is imprecise enough that fractionation and filtering must be done with a certain amount of empty tank volume to work with and be carried out with tricks and tweaks of sub-tank temperature gradients. The Engineer has to play the fuel tankage and piping like a gigantic pipe organ, and the performance will vary with every ocean, iceball, or gas giant source of unrefined fuel stocks. Since most Engineers have better things to do with their their time, they'll tell any ship owner who cares to listen to give up the tonnage and install dedicated refinery hardware, or just buy refined fuel.
