Most of the new app features are tied to OS-wide and OS-APIs wide capabilities, so they can't release "just Notes" without the OS-level frameworks that support those features. Take for example the PDF editing/support in Notes now. Or the Pages compatibility. Or Note widgets for the desktop, etc. Similar case for Safari, as they offer the webkit widget and JSCore as an OS-level APIs too.
Plus of course everything is tested together (which is what Linux distros also do. They update their apps for minor releases and bugfixes but not major releases for the same distro).