As stated they are similar engines with the same firing order and same 6.2 liters of displacement. They have the same compression ratio, same block, same bore x stroke, but that is where the differences end.
The LSA offers 556 horsepower and 551 lb-ft of torque. The LS9 output is 638 horsepower and 604 lb-ft of torque. To support this higher output there are significant changes. The first of which is a larger 2.3 liter supercharger.
The LS9 also revs higher to 6600 rpm versus 6200 for the LSA. Now, that brings us to the internal difference. The pistons and rods are both difference. Most people assumed the LSA was much weaker (it is, but not weak as recent 900+ whp stock internal results show) and although its internal parts are of lower quality than the LS9 they are very strong. The LSA does not have the same titanium forged rods but forged powder metal rods. The pistons in the LSA are hypereutectic aluminum alloy. The LS9 piston is forged.
The chart below lists a comparison between the two motors and pictures of some of the internal components are included for reference.
LS9 piston on the right, LSA on the left:
LS9 on the left, LSA on the right:
LS9 forged titanium rod:
LSA powdered metal rod: