Remember - if you equip an item and hit "simulate", it will give you an accurate result. So, if you think you should be using an item with agil and/or arpen over strength, equip the item and run a simulation to compare the results.
The item lists are just showing estimates of the relative DPS. Right now they are slightly favoring strength, due to the complexity of factoring in the hard and soft crit caps for our estimations. We are working on improving those estimates, and hope to have an update out soon.
It is not that easy. One item vs another is just few points difference, and the variability with default settings is around 60.
I tried 3 runs with 10000 iterations (variability +-6), with different gemming:
full str: 10072
full agi: 10082 (65% crit before mongoose, idol, DV and DBW procs, thus partially past soft crit cap)
full arpen: 10146
The estimations were not very helpful (yet). Maybe it would help if you explained how are the estimations done? If its not secret. As it is now they are wrong for my profile, and testing each item with 10000 iterations is not practical.
Also while i understand why the tool would underestimate agility due to soft crit caps, i dont see why it would do the same with armor penetration as i dont have hard cap yet, and i have no arpen-proccing trinket. Any chance you forgot to update DBW which is not proccing armor penetration anymore? When i had full arpen gemming, it said that strength is the best stat to gem, and it switched back to armor penetration when i regemmed half of the gear.