The difference in damage reduction is even bigger then it seems at first glance because, you're probably talking about roughly a 63% vs a 70% damage reduction scenario.
This basically means a 100k hit becomes a 37k hit at 63% and a 30k hit at 70% damage reduction.
so let's compare 37k and 30k, 30k/37k=0.81. In other words: that about 19% less damage because you stack armor.
Keep in mind that this is just guaranteed reduction and not actually less total damage taken. The numbers are also off because the BiS list wasn't very good, some of the armor parts will still be used, for example the legs (unless you are going for threat or something). A lot of this also comes from trinket choice alone. The difference really should be evaluated by piece.
One thing about factoring magic damage into EH, that calculation really isn't very useful for a lot of encounters. In many cases, it does not matter what part of your overall damage taken is magical. Magic damage is usually more about burst and you should look at how likely that is going to kill you. Good examples for such encounters are Sartharion or even Malygos.
TBH stacking the armor gear will, in most cases save for some heroic 25m pieces, give you the most stamina as well. The times where you would want more stamina than armor would usually culminate in switching trinkets, perhaps rings if you're using TOC or Ony stuff, and a weapon if you're using the one off Anub 10. Either way you will have close stats, switching some gear out for different fights is or should be common practice.