There's a few reasons behind this.

1. Stack and reach as defined are simply not very good measurements of how a bike will fit, because they are not independent. Take two bikes with same reach, but one has a 3 cm more stack than the other. By the time you've added 3 cm of spacers to the other bike, its actual reach will have decreased by 1 cm. So when a smaller size frame has less stack and same reach, it is actually shorter than the bigger size.

2. The actual sitting position on the saddle is typically behind the centerline of the seat tube. This means that the lower the saddle goes, the steeper the seat tube needs to be to keep the actual angle between the sitting position and the bottom bracket the same.

3. Where the wheels are relative to the bottom bracket is important, but not because of toe strike (I've always had some toe strike on my bikes, and I've always had sizes 56-58). Wheelbase and chainstay/front center measurements have major effect on how a bike will handle, and to get a road bike that handles like road bikes do, they need to be within a certain range. If you try do simply linearly downsize a frame while keeping all the angles the same, the wheelbase quickly becomes too short to handle well. If you extend the wheelbase by making the head tube angle slacker and front center longer, but keep the seat tube angle the same, you end up with too much weight on the rear wheel and not enough on the front. If you lengthen the chainstays and shorten the front center to improve the weight distribution, you decrease the responsiveness of the bike to steering "from the hips". So you leave the chainstays shorter and the front center longer, and you make the seat tube steeper to move the center of mass forward, and thus extend the measured reach - and you get a bike that balances and handles the way a road bike does.

4. Finally, some manufacturers simply have some strange ideas about bike geometry and how it should scale through the size range (or, worse, they don't really put that much thought into it).