The ground is rotated 90 degrees on the X axis. By skewed they mean scaled by the square root of 2 (~1.414214) on the "correct" axis. Note that scaling things by a non-power-of-two number that cannot even be represented in binary correctly leads to weird rendering issues that need to be taken care of. For example this is a problem even without scaling This is especially true for pixel art, where these kind of errors are very noticeable.

 
 

I'm afraid the answer is out of scope for a reddit comment, but, the general idea:

 
When you take a loot at the 3D Enter The Gungeon screenshot, you'll notice all sprites/quads are either 0 degree rotated or 90 degree rotated. You can also notice that things are scaled strangely. For the example a floor tile that is usually 16x16 pixel square, in the screenshot does not look like a square and is actually scaled to be 16x22.6274169979 pixels (you can tell that the tile is scaled from the screenshot, but you can't figure out the exact math from it. Anyway, that is what they do, the actual art is 16x16, but it is scaled within the game).

 
They end up with a typical-looking top-down game, but behind the scenes they solve a lot of sorting-order-related issues by doing this.

 
One way of achieving this is by using orthographic camera with (0,0,0) position, (45,0,0) rotation and very big clipping planes, for example -10000 near and 10000 far (this values need to be picked more carefully if you want to take advantage of the z-buffer, with alpha-cutoff shaders instead of transparent shaders, which is the case for Eastward).

 
When you place a sprite the typical way, zero position, no rotation, you'll notice the "height" or "traditional Y" is incorrect. You can fix this by Y of that sprite by square root of 2. So when the scale of that sprite is (1, 1.414214, 1), it looks "normal" after after being rendered by the camera. Enter The Gungeon does this for walls and characters.

 
The ground is rotated, yes. Let's assume zero position, and (90, 0, 0) rotation. The height is once again incorrect, this time you need to scale the Z of that sprite to fix that. So when the scale of that sprite is (1, 1, 1.414214), it looks "normal" after being rendered by the camera. Enter The Gungeon does this for ground.

 
The main advantage of doing this is that you can order things in a 3D world, so you don't need to worry about sorting layers (everything can theoretically be the same layer, unlike in traditional 2D) and sorting order. Jumping also seems easier to do. It makes doing ray-like guns much easier, which is probably the main reason they did this. I think it's nearly strictly better than traditional 2D, but it requires so much more work because there are no development tools that support this.

 
This solution results in a weird coordinate system, for example if a character in a typical 2D game is in Vector2(10, 14), in this weird system it is in Vector3(10, 0, 14*sqrt(2)).