There are 4 Symfony events you can use to add your own implementations of one of the 4 module types. All you have to do, is to provide a class name accessible to the autoloader.
civi.xdedupe.finders- Finder modules
civi.xdedupe.filters- Filter modules
civi.xdedupe.resolvers- Resolver modules
civi.xdedupe.pickers- Picker modules
This allows you implement very specific workflows to suit your organisation's needs.
But it also enables extension developers to ship deduping "instructions" regarding their custom datastructures along with the extension. This could be new criteria to be used to identify potential duplicates ("finders"), for example a special ID supplied by this extension. Or, for example, it could provide the instructions on how to properly and consistently treat this custom data in case of a contact merge (resolvers).
You can have a look at an example where custom modules are being added by another extension HERE.