Note that the JRE installs to /Library/Internet Plug-Ins/JavaAppletPlugin.plugin only, so it cannot easily be used by Java desktop applications and appears to be for applets only.
It also installs a System Preferences plugin that opens up a custom Swing-based settings panel that looks awful on a Retina MBP. It tries to replicate the look of the standard Apple Java Preferences app, but is confusing because it doesn't affect the system Java that you'd see when doing 'which java' from the command line.
The installer script then sets the permissions on /Library/Internet Plug-Ins/JavaAppletPlugin.plugin to root:wheel. This is the same as the bundled Java installations.
This does seem weird to me, as you said the java executable by default gets installed to /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Home/bin/java. Whereas the java executable within the jdk package gets installed to /Library/Java/JavaVirtualMachines/jdk1.7.0_06.jdk/Contents/Home/bin/java.
The images compressed a little on upload, so it actually looks even worse than in the image. The contrast between the sharp text everywhere else and the fuzzy Swing window is jarring.
It also installs a System Preferences plugin that opens up a custom Swing-based settings panel that looks awful on a Retina MBP. It tries to replicate the look of the standard Apple Java Preferences app, but is confusing because it doesn't affect the system Java that you'd see when doing 'which java' from the command line.
The installer script then sets the permissions on /Library/Internet Plug-Ins/JavaAppletPlugin.plugin to root:wheel. This is the same as the bundled Java installations.