As long as you are qualifying based on number of flights then the price doesn't matter, but as you pointed out it has to be a flight that you pay for. I don't think it is uncommon to make an "A-list" run around this time of year for people that are one or two legs away from qualifying. I made a RT from MDW to MSP last year for this purpose since the fares were so low. (Using points for one leg since I only needed an additional flight.) If you are going for points to qualify, then obviously the more expensive flights count at a higher rate, and BS flights count 12x points instead of 6x points (in addition to costing more).
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