Why does OpenSCAD fail to cut holes in polygon sides that are exactly the width of the wall?
openSCAD simply allows having surface solutions that result in a wall of 0 thickness. The walls appear to clip in those areas and can at times be seen from both sides, like in your example:

A 0 thickness wall is also exportable into an STL as a set of triangles spun up by vertices that are in each other's plane but have inverted normal vectors for the two sides - which means that the construct exists for the computer - and I have used this in 3D designs for a hologram-effect, even if it does not result in a physically possible property set.
An example of that effect is this cube (made in blender), that has the back wall purple, all others are grey - and the internal wall is at the same X-value as the back wall. You see the grey wall clipping despite the normal of it pointing to +X while the normal of the purple wall is into -X.

By having your cookie-cutter extrude not just to but through the back wall, you force a solution that disallows the 0-surface solution and thus solves the problem of creating those artifact walls.
Note that the 0-surface wall persists in the slicer preview:


But rest assured: almost all slicers ignore walls that are too thin to be printed, and a 0 thickness wall especially is ignored: