As far as the difference goes, you are right. Phonegap is an implementation of cordova. And she goes hand in hand. The documentation also skips from one to the other, so you can say that the phone call is a son who looks exactly like his cordova father.
Hybrid applications have their own limitations, for example, from now on you cannot create widgets using hybrid applications. You also need to rely on plugins to access parts of the device, such as location, notification, etc.
Having said that plugins are open-source and well supported by the community.
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