It would be nice to have the option to compare all such objects on definition and not on name.
Please use your MOS account and submit an enhancement request to the Oracle database group.
Sql Dev uses functionality provided by the standard Oracle supplied packages (e.g. DBMS_METADATA_DIFF) so any changes to those packages would have to be done by the DB group within Oracle.
Thanks for the answer. Of course there is no high urgency for this change, but with a growing usage of e.g. the identity column sequences it might make life easier.
I will make an enhancement request on MOS later (after finding all desired cases where system generated names may occur).