There's a typo I want to correct in there. If the airport has an operating control tower you do have to talk to them to get clearances to operate (taxi out of parking, take off, land, enter their airspace, etc).
Of course there's an exception to everything. If you don't have a radio or it is broken, there are procedures where the control tower shines a light at you and you see green or red and depending on the light pattern they can provide clearances to aircraft without radios. To take-off like this you'd need to call up the tower and make arrangements and for landing you'd in theory have to wait until they noticed you circling and you got your green lights.
Any pilot can call for a weather briefing prior to a flight, but most don't. For most private traffic, the pilot never talks to anyone other than the other pilots in the area advising what they are up to... and technically don't have to do that even if the airport doesn't have a control tower (most don't).
It is extremely unlikely that the weather briefer or ATC would inform pilots of mountain phenomena because it's like warning pilots that bright blue light shines from every possible direction when not obscured by clouds. It's just a given.
There are basics about mountain flying you are taught regardless of where you learn, and any west coast pilot has to deal with these realities if they go anywhere inside of the coast. I've fought off 400 ft/min downdrafts on flat land 800 miles from a mountain.
Fossett would have known very well about mountain waves. He would not have continued towards the peak of the mountain if he was sinking. The probable cause report doesn't really inform us of anything more valuable than "the sky is blue".
The autopilot isn't HAL, or anything like it. Autopilots execute a series of instructions which are programmed at the start of any flight and modified as necessary en route.
Essentially, the autopilot follows a script while using the instruments to maintain the airspeed, altitude, and climb/descent rate that is programmed. They also entrust it with turning off the seatbelt lights at 10,000ft.
This is the easiest part of flying and the most mundane. The auto-pilot accomplishes this through something very similar to a bunch of PID controllers connected to the most basic sensors.
That may not prevent it from being called a robot... but it's really the reverse scenario of what you present. The robot takes care of a relatively trivial task while the pilots take care of "everything else" (flight rules, fuel, traffic, coordination, navigation, etc etc).
I tell them to turn to the study of mathematics, for it is only there that they might escape the lusts of the flesh. -- Thomas Mann, "The Magic Mountain"