Yes Brian. We did a check and found that some tables are missing from the secondary DB. Below are few of them. But the size of the tables which are available in both have the same size. Only the once that missing contribute to the size difference.
dbo.TASKSTATE
dbo.CONTENT_EVENTS
dbo.SEM_AGENT
dbo.SEM_CONTENT
Microsoft SQL Server 2012 - 11.0.5058.0 (X64) Standard Edition (64-bit).
SEPM version 12.1.6