Hey, I'm from Ask Mr. Robot.
We actually do account for procs on trinkets. In fact, we have a very in-depth analysis of trinkets. We simulate every trinket for every class to get the average uptime for each stat. Here's a list of the results: http://www.askmrrobo...terbeastmastery
We then apply your stat weights to the average amount of stat you get from the proc. This is how we decide what is best for you.
Mr. Robot also takes into account your race, talents and professions, and your custom options when figuring out your BiS. For example, draenai get 1% hit, so they might end up with a different BiS than someone who doesn't get the extra hit. If you're a JC, your BiS might also change, when compared to a LW.
Our lists are dynamically generated, custom to YOUR character and settings. Doesn't get much better than that