What comes to Diablo 2, it is truly isometric. What i have seen its graphics, they are diamond shaped not rectangles. But its graphics are not only tiles or diamonds, it uses lots of different shaped and sized even very large transparent sprites. Though i am not sure how collisions work with D2 :?:

SC and Diablo both are isometric games. D2 has even option render it with 3D perspective. Both have units rendered from certain angle not straight top in any case.

What comes to flying units, only way to tell they are flying is their shadow that is placed under them. What's really interesting about it, is that units don't move up when they go higher only shadows move down A brilliant way to make unit selection and movement easy and effective.

Edit: SC is still isometric game no matter it is rendered with tiles...