Is this right?

I was tinkering in Mids' to make a ranged softcap build for my level 42 fire/fire/fire blaster, and came across something weird. I've got 5 full sets of Thunderstrike for the total 3.75% bonus. I also stuck a 2-set of Blessing of the Zephyr in Hover and Combat Jumping. According to Mids', the 1.25% ranged defense from the BotZ sets still work, even though the Thunderstrike sets have a 1.25% bonus from being 3-slotted. All I can figure is that since the 3-slot bonus is actually a 2.5% E/NE defense bonus, it stacks with the 1.25% ranged from the BotZ despite the fact that the actual bonus to ranged is the same.

Is this how it actually works, or will I need to watch my builds carefully to avoid this?

I believe they are considered different in terms of the rule of 5, given different names (Small ranged boost vs. small E/NE boost, perhaps?). It should still be fine, since, if I remember correctly, when they changed the BotZ set bonuses, they set them up to be useable along with the other sets, like Thunderstrike.

They're not the same bonus.

The BotZ bonus is 1.25% Defense (Ranged), 0.63% Defense (Energy), 0.63% Defense (Negative).

The Thunderstrike 3-slot bonus is 2.5% Defense (Energy, Negative), 1.25% Defense (Ranged).

Everything listed needs to match up to be considered the same bonus; just a part of it having the same effect isn't enough. Mids' is usually pretty good about letting you know when the Rule of Five is broken - if you don't see the red "cap" message in the right hand pane of the set bonus window, you should be okay.

Awesome, that's what I was hoping for. Thanks!