EDIT: just reread this...you are dealing with new work, not old work. What you might want to do in your case is grab the one of the two braces I linked to below so that the height of box is referenced off the drywall instead of the bottom of the joist. I'll leave the rest of the info up, in case someone is having similar trouble.
I just had to deal with this issue, and you are right, most old-work ceiling fan mounting kits don't accommodate engineering joists well at all. I ended up getting both a kit from
Lowes and from
HD. The Raco/Lowe's version did not work at all, even though it looks like its supposed to. It has a fat surface that looks as if its supposed to rest on the lip of the lower beam of the joist. The problem is then you have no teeth digging into the joist, so no matter how tight you try and crank the cross beam, it can still be easily forced out of place.
The Westinghouse/HD version has a circle of teeth that is large enough in diameter so that at least the lower third of the circle grips the lower beam of the joist.
Jake