I played through those events even further back, so I’m less sure of those.
However if that’s the case, why does the New Dawn out of contact stuff cause our faction to go nuts while the others don’t?
I may be remembering this stuff wrong - from what I can remember the faction reaction to the events you mention are in the mission reward text as opposed to a cutscene.
I may also be blowing up the later event because of my visceral reaction to that cutscene. It more or less completely blew any sympathy I had for my handler - although that’s probably because of my head canon.
My guess might be the length of time? It is somewhat hard to judge how long we are there until Mr. Knick-knack gets knackered. Apparently long enough to miss out on entire Antarctica expansion. Of course if we get too picky, surely they would’ve seen us flying for Africa on a dinky little turboprop which would’ve taken days to merely get there. I suppose one can hand waive and say Che’s plane was also somehow protected by the wards.
If I remember correctly, I got chewed out by KG by being unavailable during the first (?) story choice. Although we don’t know how big the timeframe is, it can’t be too long, as the story picks up relatively fast again.
So, being awol -or out of touch- for an extended time frame in New Dawn, the handler is of course more distressed/angry.