Can you describe what you are running into a little bit, just so we can verify there isn't a way around this for you in particular.
In general what this article is refering to isn't something you can really fix. If the application is specifying a source address then that's what you'll see come across, there isn't really a way to fix that from a GlobalProtect administration side of things. You could potentialy route this traffic around the GlobalProtect routes, but this would be a highly manual process and would likely have a maintenance cost associated with it as far as maintaining those routes are actually correct.
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