I can't see a single thing pointing to a military theme to the ride
A military organisation, wearing body armour, with a helicopter and an armoured vehicle that you almost need to walk around to get into Forbidden Valley are central to the entire marketing campaign. That's quite a big single thing wouldn't you say?
You're right, they could just drop the whole thing once the ride opens and forget it never happened. I hope they do, or they at least inoffensively just linger in the back ground somewhere mostly out site (there seems to be this obsession with roller coasters needing some sort of "back story" by some, which is fine if that's what you're in to). But I wouldn't put money on that being a certainty would you?
Besides the context of the post was about the look and feel of the ride area itself and FV surrounding it. That's more important to me. I couldn't care less about any story behind these things. JW always said it was "nonsense", it really was just an excuse to make a cool looking coaster in a pit. I'd very much prefer there not to be people dressed like armed police officers, tanks, helicopters and stuff around the ride. I don't really care about why an alien creature, who happens to look exactly like a B&M inverted roller coaster, is pinned down with steel that just so happens to look exactly like B&M invert coaster supports and the back story behind who put them there. I don't care why the Beornan decided that the process of sacrificing guests by burning them in a Wicker structure had to involve a GCI wooden coaster as the the delivery method. It just looks cool.
I hope (but not expect) that all this Phalanx stuff is just marketing to hype things up and that we just end up with this mysterious alien monster bursting out of a pit for no reason whatsoever, leaving the blanks to be filled in with guests imagination if they so choose. Rather than just turn it in to Call of Duty: The Ride.
On the other hand, although they've stopped short of ruining everything as I've heard it's actually rather good, I can't help but feel like all this fan service stuff is over reaching ala Alton Manor. No one other than Thoosies care who Emily Alton is and some of the "Easter Eggs" around that ride seem cringeworthy. The best fan service would be to sort the state of the park out, but that would cost over £100m whereas putting up a sign saying "Wardley Estate Agents" costs a few quite from Leek Signs. But I digress, it would be good if they didn't pollute the theme of Nemesis with all these military people for the hell of it.