What is the difference between embedding objects in my project and saving the project as a PLA?

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Embedded objects exist only in that particular project and can be used only in that project. (In contrast, objects of a linked library can exist in several projects.) If you delete an object from the Embedded Library, it is gone. If you edit the script of an embedded object, that modification will occur right there, in the Embedded Library of that particular project. In contrast, a PLA file is read-only, and the objects must be extracted before they can be edited. Such edits will affect the object in all projects which use it, not just the project you are working on.