I assume the machine cancel could only strike a stamp in the upper right hand corner of the envelope. Back in the day that these covers were produced, a collector would have to submit self addressed envelopes to the Postmaster along with their request (and remittance) covering the requested stamps to be affixed. I can only assume the US Post Office clerks elected to put the stamps on the right hand side of the cover (which makes perfect sense) but in order to do so it had to partially obscure the rather large return address written by the collector. In order to "tie" the stamps to the cover with a postmark, they had to use a duplex handstamp cancel for the bottom two stamps that the machine cancel would not have otherwise reached.
[Edit]: Here's another example taken from McCusker's FDC web site. This example (same addressee and same Concord Junction cancellation) is currently on their website for a "sale price" of $90 (reg. $100):
