Rarefied items are turned in for gatherer scrips. Non-rarefied collectors items are used for custom delivery turn ins. The two you mentioned specifically are for M'Naago's custom deliveries.

For both, when you harvest them you wanna get their rating as high as possible. The higher the rating, the better rewards you get from turning them in (and rarefied ones generally need a minimum quality to even turn in, custom deliveries tend to be a bit more forgiving.)