Faces of the elements of block models go up to black if there are blocks next to them / Block lighting is applied incorrectly

The bug

If a block model has elements inside or outside the block's boundaries, their faces will go up to fully black if you place blocks around them. All faces of model elements are treated as if they were directly at the block's boundaries.
Important note: this bug is partially dependent on ambient occlusion (smooth lighting). If the smooth lighting is turned off, only the top and bottom faces get darker. If it's turned on, the west/east/north/south sides also get affected.

Without smooth lighting:

With smooth lighting:

Steps to reproduce

Install the attached test resource pack and try placing chiseled quartz blocks next to each other.