[Disclaimer: This answer is a guess, there might be something else going on.]
When you boil water in a large enough pot, the water will flow in a toroidal shape, that is, it will rise from the bottom at the center of the pot and go back down at the edges of the pot. As the water flows, it carries some pastas with it, & the pastas are usually alligned with the flow (like most logs flowing in water). The penne has less weight and moves faster, and if by chance, it happens to go through a rigatoni in a collision, it will stay there because once inside the surface contact between them increases and they stick to each other. Plus there might be some turbulent or flowing behavior inside the pasta that makes the water flow faster inside the pasta than outside, which would increase the chance of the penne entering the rigatoni one close enough even if not perfectly aligned. Give it enough time (8 minutes?), and most of the penne will end up inside the rigatoni.
