One thing to consider for option 1 (collar into rafters, queens into collar) is the shrinkage of the collar. Is has a bearing surface on both the top (to the rafters) and the bottom (to the queens). As is shrinks, it may transfer some of it's load out to the rafter feet.
Another thing to consider is ease of raising. Again, with option one, you may want to fly in the collar/rafter pair as a sub-assembly. CB.
