The point on environment made me think of Civ, though turn based, in which affecting the terrain and fighting are somewhat linked : clearing terrain for faster transport, nuking an enemy city.. But it's nowhere near what's described in the article. Then you've got the total war franchise in which terrain is essential to tactical fighting, but still, terrain can't be modified to affect the fighting itself (and there are bomb units and cliffs, so the opportunity would be here). Maps are still very shallow in the strategy genre, it seems that they have resources and movement properties and that's often pretty much it.
While we're talking oldies, this made think of Master of Magic (turn based), which had parallel universes, another concept that is very much under-utilized. And 'parallel universe" is a theme up for the round 2 of voting for the upcoming ludum dare.
In the Civ lineage, Alpha Centauri does have far more extensive terrain modification. Not using the mechanics mentioned in this article, but you can raise and lower terrain, and doing so raises/lowers surrounding terrain too. It can be highly effective to use modifying territory as a strategy.
Not only does it alter movement points, it also alters weather patterns, and so resources gained.
A highly successful strategy (especially when playing agains the AI, which doesn't understand this pattern) can be to create straits up against stronger enemies to force them to rely on seafaring troop transports (that area easy to take out). And when your land units are strong enough to create land bridges wherever you want to go and build railroads instead of sending naval units and transports to attack enemy cities.
What about Bullfrog's Magic Carpet? It had resource gathering and terrain modification as core mechanics. I think it also had base building. It was first-person though.
By the way, Magic Carpet is returning as Arcane Worlds. It's looking very good, and has some new effects like good looking water spells. I described it in more detail here:
You might like TA Spring (a full 3D remake of Total Anihilation). It features fully deformable terrain, some of the games on top of the engine even let you terraform! Elevation plays a part in combat mechanics - high ground makes a difference. You can also block enemy shots by terraforming the land since everything runs on a physics engine.
While we're talking oldies, this made think of Master of Magic (turn based), which had parallel universes, another concept that is very much under-utilized. And 'parallel universe" is a theme up for the round 2 of voting for the upcoming ludum dare.