Macbook 12,1 (OSX 10.11.4) will not boot SSD clone of OSX 10.9.5 from MacbookPro 11,1
You say the only difference between the two models is the size of the drive. This is an incredibly naïve statement. Although, I have not checked in depth, it would be a safe bet next model differs in hardware beyond the drive size. 

Let's look at the chronology.


OS X 10.9 is released on November 22, 2013
MacBookPro11,1 is either a Late 2013 or Mid 2014 model. Should be
shipped with OS X 10.9.
OS X 10.10 is release on July, 24, 2014
MacBookPro12,1 is either an Early 2015 model. Should be shipped with
OS X 10.10.


When OS X 10.9 was released, most likely this version did not contain the software (drivers) for Macs not yet shipped. So installing this operating system on a future MacBookPro12,1 model should result in failure.

The opposite would likely succeed. You should be able to take OS X 10.10 from a MacBookPro12,1 and run successfully on a MacBookPro11,1.

How about upgrading OS X on the older machine before running on the newer machine?