In the XPages environment, there are two kinds of documents: the standard Document class you get from normal Domino API operations and DominoDocument (styled NotesXspDocument in SSJS). Many times, these can be treated roughly equivalently: DominoDocument has some (but not all) of the same methods that you're used to from Document, such as getItemValueString and replaceItemValue, and you can always get the inner Document object with getDocument(boolean applyChanges).

What's less common, though, is going the other direction: taking a Document object from some source (say, database.getDocumentByUNID) and wrapping it in a DominoDocument. This can be very useful, though, as the API on the latter is generally nicer, containing improved support for dealing with attachments, rich text and MIME, and even little-used stuff like getting JSON from an item directly. Take a gander at the API: com.ibm.xsp.model.domino.wrapped.DominoDocument.

It's non-obvious, though, how to make use of it from the Java side. For that, there are a couple wrap static methods at the bottom of the list. The methods are overflowing with parameters, but they align with many of the attributes used when specifying an <xp:dominoDocument/> data source and are mostly fine to leave as blanks. So if you have a given Document, you can wrap it like so:

Document notesDoc = database.getDocumentByUNID(someUNID);
DominoDocument domDoc = DominoDocument.wrap(
	database.getFilePath(), // databaseName
	notesDoc,               // Document
	null,                   // computeWithForm
	null,                   // concurrencyMode
	false,                  // allowDeletedDocs
	null,                   // saveLinksAs
	null                    // webQuerySaveAgent
);

Once you do that, you can make use of the improved API. You can also serialize these objects, though I believe you have to call restoreWrappedDocument on it after deserialization to use it again. I do this relatively frequently when I'm in a non-ODA project and want some nicer methods and better data-type support.