You have to consider what is between you and the enemy unit at all times in this game. It's no different than how with infantry combat you have to think about cover between you and the opponent.
You know that being on the low ground means your shots are more likely to not hit your opponent. Therefore it becomes a part of your tactics: controlling the high ground means you are better protected, while attacking from low ground will be much harder.
You have to stop looking at the game with an a-move mentality. The best part of this game is that where your unit is standing is actually fucking relevant to how it performs. If you position an artillery piece next to a house, it might hit the house instead of where you wanted it to. If you try to throw a grenade, it may get caught up in buildings or hedges in its path. You have to think about these things all the time in this game.
Also, tanks generally don't have much ability to adjust their aim in terms of verticality. A few degrees of pivot at most. Not to mention that units on high ground are literally more difficult to hit with any sort of ranged weapon and that has been true for thousands of years or warfare whether you're using bows, guns or tanks.
Agreed that it's good that how current system rewards use of terrain, but disagree that what you're describing is really how it's working. Right now it's less that players with better elevation get in advantage, and more that tank behavior has profound troubles even on nearly flat terrain with just tiny hills. In this sense it's less like cover mattering for infantry and more like the pathing problems that vehicles have suffered from. Like pathing problems,it certainly DOES promote more micro, just not in a good way.
Also, I know that certain aspects of OKW base defense are unfair, like how they outright deny so many air abilities, but with the current system they will often do nothing but fire into the dirt against ground units no matter how they are placed. So at the moment they are broken against air strikes (in an OP way) and broken against ground units (in an UP way). Building the Flak emplacements would become more viable if their behavior got reworked, nothing too extreme, just make it so that it requires a bit more elevation for them to fire helplessly into the dirt.
I say keep it the way it works now, but make it less extreme, so you actually need a discernible terrain advantage to benefit from it.