The behavior seen in this repro is actually expected but needs some explanation.

For performance reasons, Alpha tested geometry always needs to be rendered in two passes
- Depth prepass
- Color pass with depth test set as EQUAL and no alpha test.
The reason for this is that on most modern GPUs, whenever a shader contains a clip/discard instructions, the HiZ optimization is disabled causing huge performance loss for layered alpha tested geometry like foliage. By rendering alpha tested geometry as described above the color pass (which is the heaviest in term of performance) does not use clip instruction anymore and can be rendered efficiently.
The consequence is that with two perfectly overlapping objects, the alpha tested color pass will pass the depth tests making it visible. The artefacts displayed in this bug are actually regular z-fighting artefacts.
The only solution in this case is to add a small offset/scale to avoid the perfect overlap.