If I save template of a list, the stp file generates Manifest.xml but if i save a template of a Site, for the same list, it generate Schema.xml. Whats the difference? the two seem to be working in a different manner! Also, the Site Template (wsp file) has ElementsContentType.xml but List Template (stp file) doesn't have it! Why? Manifest.xml replicates the exact structure but Schema.xml seems to default to the default settings of the Content Types of the destination web. why or how? even the content types referred for the same list vary between List and Site templates! Why?
Site Template contains the whole Site and the list (also Content Types) if you have a List Template this only contains the List. If the List Template would contain also the Content Types from the Site it was created from there could be possible issues when trying to create a new list from this template in another Site. To prevent this issue, you get a different version of the Listtemplate when you only make a List Template.
Maybe this helps you a little in understanding? https://msdn.microsoft.com/en-us/library/office/bb802990(v=office.12).aspx