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I don't see any reason why it wouldn't be. The only problem you're going to run into is the hundred of other thousands of people who may have put that Pokémon into the GTS. I would just borrow a secondary DS from someone and trade them directly. It'll be a lot less stressful that way. :D
Like said, I don't see an issue in compatibility between DPPt and HG/SS through the GTS as they can communicate via Wi-Fi and Wireless regardless. So, yes, you will be able to connect through the GTS without problem, no matter the version.