Yes, there are few options to make use of related objects.
Scenario 1. Related object is a one-to-one relationship
For example, if we deduplicate accounts and want to make sure that the master record is an account that has an active owner then we can use the following rule
Scenario 2. Related objects are one-to-many relationship
Create two datasets,
Dataset #1: Accounts with Active Contracts with the following SOQL Filter
Id in (SELECT AccountId from Contract WHERE Status = 'Active')
Dataset #2: Accounts without Active Contracts with the following SOQL Filter
Id not in (SELECT AccountId from Contract WHERE Status = 'Active')
Then, create a cross-object dataset where Parent is Dataset #1 and Child is Dataset #2.
Note: The following example helps resolve "When merging portal enabled accounts, the master record must be portal enabled." Salesforce error.
Another practical example of this is selecting a contact with enabled Portal User to be master record:
Dataset Portal User Contacts
Id IN (SELECT ContactId from User WHERE IsActive = True AND IsPortalEnabled = True)
And a dataset of Other Contacts:
Id NOT IN (SELECT ContactId from User WHERE IsActive = True AND IsPortalEnabled = True)
Create a cross-object dataset where Parent is Portal User Contacts and Child is Other Contacts.
The duplicate groups in the cross-object dataset will have master records with portal users and the merge should go through.