GitHub always has the latest greatest of course. The Marketplace usually lags a bit behind because Epic takes their time updating it.
One gotcha to be aware of is that the content of your workbench window might potentially get lost during update. It is stored in the file
<SkookumScript plugin folder>/SkookumIDE/Scripts/workbench.sk. Pulling latest from GitHub is safe and will not change your
workbench.sk file, but updating from Marketplace, or moving to an entirely different version of UE4 might lose its content. If you have important script snippets in your workbench, you might want to copy this file to a safe location prior to updating.