Handling sentinel data in python ( working with snappy)

Regarding the ArrayIndexOutOfBoundsException I can’t help you. At least I would need some more information. Is more printed as just the exception. Some stack trace below.
You might be right that it might be related to the multi size issue.

Subsets can currently only be done on product where all bands have the same size. In the future this should also work for multi-size products.
Before you Subset you should use the resample operator, to make the bands equal in size.

HashMap = snappy.jpy.get_type('java.util.HashMap')    
snappy.GPF.getDefaultInstance().getOperatorSpiRegistry().loadOperatorSpis()
source = snappy.ProductIO.readProduct('G:/EOData/Meris/RR/MER_RR__1PNBCG20050709_101121_000001802038_00466_17554_0001.N1')

parameters = HashMap()
parameters.put('paramName', False)
result = snappy.GPF.createProduct('Resample', parameters, source)

You can get the available parameters either by calling gpt Resample -h on the command line or by open the Resample Operator in the Desktop App and the go to the menu File/Display Parameters.