How are interleaved paired reads treated in Metalign?

I see in the paper and in issue #31, that paired reads can be run in Metalign after interleaving the reads.  

When an interleaved file is run in Metalign, is each read considered separately? 
Are the pairs combined somehow? 
Are the results from each read in a pair considered and a call is made to determine the taxonomy when R1 and R2 don't have the same hit?