This is exactly what I'm doing for one of my customers now.
We're importing the data into a central database, tagging with source.
Dashboards are embedded with a hidden filter that selects the correct source/sources.
We're also doing some separate instances of Metabase that work on a separate database containing one or more sources.
We have a single source Metabase configuration that's just rolled out for each instance. Only a case of setting the database connection.