This isn't a situation involving polyploidy. As far as we know all snakes have 36 pairs of chomosomes: 20 micro, 36 macro. Hybrids between python species occur successfully so often because of the similarities. Many of them are even fertile.
And its not the chromosome as one whole that codes for traits, its the alleles on the chromosomes that do. There are very many alleles that go into each trait that an organism possesses. Some hybrids may look more or less like one of the parents, but that goes for any organism, including those that are not hybrids.
And its highly likely that most python species have very similar hemipenes. Given that many can interbreed successfully and produce fertile offspring the reproductory organs must be similar.
I hope that this made some sense. If any of it is unclear or anybody has a question let me know!
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