Private app authentication by a collaborator user

Shopify Partner
9 0 3

We have a private app that is authenticated on the store level, which requires the authentication of the store owner- however, one of our customers is an agency that has a 'collaborator' access to the stores of their customers and they cannot authenticate it. Is there another way to authenticate a private app, or what would be another solution? 
We would also like to understand, if the solution was building a public app- will it be then authenticated on the Partner level and have access to all the stores data?

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