This is where it gets a little complicated, when having over head components in the map. ISO is 2D so the trick is layers. All the overhead objects are on a separate layer. It make s this kind of thing possible. 
Alien Phoenix supports layering out-of-the-box.
This is sort of what I want to do for ISO bases. Top-Down and ISO for maps. This ISO layout with overhead level is what I would like to see for Phoenix USC. The editor will be functional this month so everyone will get a crack at there own map versions. Should be fun. 
For coding you should really love the in-game editor as part of the framework. It makes life so easy for a coder to have this kind of option for both the author and the user. Especially the end user.
Here I have the editor running on the Chromium web browser, 1080p at 60FPS. The game engine and editor run great in isometric mode. So will the game.
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Oh ya. Liking the lighting effects. The same lighting techniques used for top-down basically work fine with a little tweaking. Here shown testing bump mapping and such. Love the look.
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1st attempt at using Isometric mapping in Phoenix USC and a test of lighting. All seems to be moving along nicely. Off to deal with ISO ship design.
Widescreen 5760x1080
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I am working on a slightly different technique for mapping isometric tiles in Alien Phoenix. Using a volumetric approach is showing lots of promise.
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Testing here using only isometric blocks. Checkout the lighting, early but in.
Here same mapping technique but no lighting (a little on floor) and free form.
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Here is a little video showing a 48 frame ship animation in an isometric example.
All for now.
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My first ever let’s build video. A time compressed video showing how easy it is to build a project with Phoenix USC and Alien Phoenix. In about a months time I’ve made some wonderful progress.
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Current IndieDB article. On the homepage as usual.
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So… That’s basically 3D just rendered in 2D isometric?
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At it’s core it’s just 2D isometric images, not even pre-rendered images but ones I made in GIMP. 
There is no 3D involved at all, this is pure 2D with a lot of magic thrown in.
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In fact a core block. This 
used to make above.
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This is likely to be the basic level of lighting detail for Phoenix USC. I’ll be making improvements as I go to shading and alike, but this lighting model works well for real-time gaming.
Totally cool that this is all 2D.
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In w i d e - s c r e e n.
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Settled on this lighting style for now. Checkout the video featuring collision. All 2D isometrics (not 3D but flat 2D images).
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Faster bullets, better ship collision.