Aspose.Words for SharePoint is built on SharePoint technology and facilitates you to convert and combine documents within Microsoft SharePoint applications. It also has a public API and offers lots of features but when its compared to Aspose.Words for .NET, the .NET version provides huge number of features and its API is very strong.
Also you have noticed that Aspose.Words for .NET can be used on variety of platforms including Windows Azure, Microsoft SharePoint, Microsoft SilverLights, Mono Framework. This component can also be used with many programming languages including Perl, PHP, ColdFusion, Python, PowerBuilder, ASP and much more. Also observe that Aspose.Words for SharePoint is built on top of Aspose.Words for .NET.