Stock 49
No actually the Boxer and the Opposed differ in the crank layout as mentioned earlier.
The term 'Boxer' is short for 'Boxermotor' (I have seen it with various spellings and as two words as well). The term was reputedly coined by Adolph Hitler when he saw a cross sectioned prototype VW engine being motored over. He supposedly said the pistons coming together (at BDC) reminded him of a boxer punching his gloves together before a fight.
The Boxer layout is supposed to give you better dynamic balance than the opposed (what my engineer friends call a 180 degree V with its' common crank pin).
The penalty is with the more complex crank layout (generally longer as mentioned previously) you tend to run into problems with the higher order harmonics. I have read the 917s had a furious problem with the 2nd and 3rd orders, which they obviously either solved or at least beefed it up to finish the race.
I have also been told the 917 engine is in effect 2 RSR Porsche 6's joined nose to nose (on the drawing board anyway), but I don't know how accurate that is.