Why doesn’t part 30099 fit into the System?
This picture might explain the reason:


As you can see, arches form a nice circle to fit round modified plate. All fits well, except the very bottom. Making the bottom edge fit the plate/tile nicely would result in gap with a round piece. The curve of this arch brick isn't full 1/4 circle to make it flush with a tile/plate.

However you may ask "Why didn't LEGO just extend the bottom curve to full 1/4 circle and cover the stud?". This seems to be an obvious solution, but that's a different topic and we may not know which decision caused the part to appear in existing form.