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Not sure what exactly you mean by multiple entities but there is, generally, only a single global datastore defined by YANG. Then there are various datastores like running or startup but they differ in the purpose of the configuration they include, not in the set of entities they support.
If you mean configuration data for multiple YANG modules then yes, it can. However, you probably want to look at libnetconf2, this project is many years old and several ones without support.
Can your data store handle multiple configuration entities?
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