I think the author swapped problems #1 and #2. The first one (name clash between different packages) is triggered only if the binaries are called the same, that is after you fix the second one (binaries having uu- prefix).
Problem #5 is not well explained: if /usr/bin and /usr/sbin are conflated, how could cowsay not find its templates? Paths relative to the two directories are the same. For example, if cowsay is looking for its templates in ../share/cows, such relative path points to the same destination no matter if the binary is in bin or sbin.
Problem #5 is not well explained: if /usr/bin and /usr/sbin are conflated, how could cowsay not find its templates? Paths relative to the two directories are the same. For example, if cowsay is looking for its templates in ../share/cows, such relative path points to the same destination no matter if the binary is in bin or sbin.