Actually if you think about it, Meshmixer's way of aligning a surface to a plane is a lot easier and more flexible than NetFabb.
While NetFabb makes it easy to rotate something in 90° increments, things get a little more complicated when you have odd shaped objects. Here is an example.
Take a 20 side die like the one below. How would you line up to "20" face with the bottom so it's perfectly flat, in NetFabb. Not easy, you would either have to calculate the angle of each surface, then rotate it in those angle increments in both the x and y axis, or you would try for a free hand rotation hoping that you get it it close enough.

With Meshmixer I would simply scribble on the surface and it would align it automatically with the bottom plane.
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To print or, 3D print, that is the question...
SD3 printer w/too many mods, Printrbot Simple Maker Ed., FormLabs Form 1+
AnyCubic Photon, Shining 3D EinScan-S & Atlas 3D scanners...
...and too much time on my hands.