Hopefully someone from the review event can answer this. I'm not going to get my hopes up, because it's always seemed like KojiPro considers Reflex Mode the 'proper' way to play, but if they got rid of the instant, omniscient Alert from GZ when you turned it off it'd fix one of my big complaints about the game.
Honestly, they had it perfect fourteen years ago in MGS2; I don't know why they ever changed it. You get spotted, the enemy retreats and calls for backup on his radio. If you can't take him out in time you get the Alert. If you take him out while he's on the radio, CP gets suspicious and goes into Caution mode. If you take him out straight away, you're home free. In Ground Zeroes, you either use Reflex mode, which is essentially a QTE prompt that all but lines up a headshot for you, or you turn it off and the entire base is alerted to your presence immediately. Like, literally before the guy who spotted you even has a chance to shout out, CP's yelling out "ALL FIRE TEAMS".
For one thing, it's not an insta-alert when a guard spots you. If you turn off reflex mode and get yourself seen in GZ, you still get probably 2 seconds before they shout. It's the shouting that alerts everyone, because obviously it would. In a small military base, if someone screams, everyone will go on alert.
But more importantly, one journalist did answer this from the May press event. Well, they didn't "answer" it, but they explained what they experienced. May still be wrong/outdated.
From what the journalist said in May, it's slightly more complicated in the full-TPP open world. Basically, it depends on the guard's situation/position. For instance, how close are they to other guards/small bases/main base?
Apparently if a guard is isolated when they spot you - maybe in the wilderness or in an empty township - they won't trigger an alert when they see you. They'll just try to take you on themselves. I swear I've had this happen to me in GZ, but maybe not.
If a guard is in a small base, like Camp Omega, they will alert all the guards in this base when they see you and shout (again, a 1-3 second window). However, someone at this base has to radio to the main base (HQ) to set the whole region on alert. When they do this, shit will get real, and you can still stop it apparently.
If you're in a large base/an HQ when you're spotted, everything goes to shit and it's full alert within those couple of seconds.
I think they removed the 'radio in' mechanic because of 1. the balancing and 2. the level design. Re balancing, imagine if you could sit on a hilltop a mile away and silenced-snipe every single guard's radio in a town before you went in. It would basically break the balance. Similarly you could knock out all the guards and break their radios so the base would, in its entirety, stop being a thread. For 2, the level design, it only made sense for guards to radio out in MGS2 when we played in small, closed-off sections of a larger base. In MGS3 and onwards, the areas get much bigger, 90% outdoors, and more interconnected, so it made more sense for everyone to get alerted from a shout. In TPP it'll make perfect sense for all nearby guards to set off the alarm if one guard shouts 'he's here'!
Anyway. My two pence.