NuGet: Difference in behavior between Update-Package and nuget.exe update?

NuGet: Difference in behavior between Update-Package and nuget.exe update?

I'm using NuGet to create a 'web framework' package containing code,
master pages, css, javascript, etc.
In an attempt to speed up the build / test process I'm running nuget.exe
update packages.config but I've noticed that it behaves differently than
the package manager console's Update-Package command.
nuget.exe update seems to leave the previous version of the package still
installed, resulting in multiple versions of the package installed
Update-Package actually uninstalls the package then reinstalls it, this is
cleaner but slower
My questions are:
1. Is there documentation about the difference / relationship between
these commands
2. Is the nuget.exe update behavior of installing multiple versions a bug?
3. Is there a better method for creating a package in one project and
updating it in another project in a fast & automated manner?