No Duplicates is a field setting, therefore validated over the value sent for the field where you enable it. There’s no “combination” of any kind when you enable it for multiple fields.
So if you enable this setting for “Email”, it will validate the value entered based on previous values saved for this form field.
If you enable it also in another field, like “Comment”, it would validate previous values for “Comment”.
Each field validation process it’s completely unrelated.
If you want to compare values for two different fields for validation purposes, you will want to create some custom validation code for it. Here’s an example: gform_field_validation - Gravity Forms Documentation
Can you confirm that the “validation” is against the entries currently stored (so if “Delete entries permanently automatically” is set, once an entry is deleted by that method a new form submission would be allowed)?