Yeah, the original "secret war" idea has been replaced although some of its spirit lives on. An open warfare setup worked better with the new mechanics we've been testing (the orbital bombardment by the aliens and the Relations gain from sharing tech with the funding regions) so we shifted the setting around to fit the mechanics.
That said, one of the things I do want to continue to emphasise in the setting if possible is that the alien invasion hasn't actually caused everyone in the world to band together and sing happy songs while holding hands - the various world powers still do not trust one another and don't particularly trust the Xenonauts either (a mutual feeling), they've just been forced into working together by circumstance.
The VIP Elimination missions are an example of this; you're literally assassinating (or capturing and brainwashing) a local VIP who is opposed to the region supporting the Xenonauts. They're not alien infiltrators; from the perspective of the Xenonauts they're simply people with misguided views that are endangering humanity and therefore need to be eliminated. And then probably lying to the locals and claiming that they were actually an infiltrator.
So, yeah, I want to retain the feeling of the suspicion and misdirection that was part of the secret war setting even though we're returning to a setting where the warfare is more overt.