Restore of Replicated Database fails with “Cannot drop the table  because it is being used for replication.” published database restoration failed once you setup transactional Replication using system Store procedures. Few work around to this problem is restore with KEEP_replication option and than drop the publication and subscription.

Is there anything we can do while setting up the Transactional replication using System SP that can avoid this issue ?
Use below query to avoid replication related SP in Transactional Replication.

SELECT name 'ROUTINE_NAME','T' 'ROUTINE_TYPE'
            FROM sys.tables 
            WHERE OBJECTPROPERTY(OBJECT_ID,'TableHasPrimaryKey') = 1 AND name not like 'MSpeer%'