What exactly does the Dependency element do?

Here is my situation:

We have the web application framework, the Framework, which my company
has developed.
            Framework.msi
                        FrameworkRuntime.msm
                        FrameworkSDK.msm

We have an extension to the Framework that targets a specific platform,
desktop browsers.  It too is built from a number of smaller merge
modules and has <Dependency> elements point back to the
FrameworkRuntime.msm.
            Extension.msi
                        ExtensionRunTime.msm (FrameworkRuntime.msm)
                        ExtensionLibrary.msm (Extension Runtime.msm)
                        ExtensionSDK.msm (Extension Runtime.msm,
ExtensionLibrary.msm)

The combination of the Framework and Extension are used by developers in
the company to build websites that take advantage of this framework.
The application has a dependency element that points to
ExtensionLibrary.msm.
            Application.msi
                        Application.msm (ExtensionLibrary.msm)

My belief, which appears to be incorrect, is that reference counting
should be happening here so that if you uninstall the Extension, the
ExtensionSDK is removed as nothing depends on it, but the
ExtensionLibrary and ExtensionRuntime should both be left behind because
Application depends on it.

For starters, is this a correct assumption?

What we're seeing is that the binaries from the ExtensionRuntime.msm are
being removed, but the ExtensionLibrary files are not.  The
ExtensionLibrary, however, is not usable as it depended on binaries in
the ExtensionRuntime.

As a note, we do our setup testing in the clean environment of a virtual
machine.

Thanks!
Rory

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