The only concern in utilizing a deeper joist seat is if you rely on the seat to transfer a wall anchorage force. The eccentricity with the deeper seat should be looked at by the joist designer. I have used up to 7 ½" deep ends (bottom of seat to top of top chord), but I was told by Vulcraft that the standard 5 ½" deep works for spans up to 64 feet for usual LH joist applications.
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