These reasons were not originally philosophical in nature: http://lists.busybox.net/pipermail/busybox/2010-December/074...
IMO, keeping /usr/bin and /usr/local/bin separate from /bin doesn’t serve any useful purpose except historical continuity. You can’t really get rid of those paths without breaking things (e.g. since /usr/bin/env is usually hardcoded in shebangs), but symlinking them together is a practical way of effectively merging them.