HI Jesus,
I never been on the Friendship Highway. But I understand, that it's a major trodden path, despite its high altitude and remoteness. This means all the pros and conts about traveling in such an environment, where locals are used of foreigners.
Dogs I experienced the worst and most ferocious wordwide in Tibet. Yes, they get big, and yes, they are aggressive and no, they are not too scared of whirling rocks. I had been forced to kill a dog during my trip.
If there are any problems with floodings, the road would be fixed soon after. And by bike, you may always still be able to cross a river, mudslide.
The altiude will affect you, if you push yourself too much. It won't be an issue, however, if you start slowly, gradually, let's say from lowland Yunnan and work your way up day by day.
Dunno about flights from Kathmandu to Lhasa, but I want to think that they would be outrageously expensive, if there are flighs.
There are certainly flights linked between Beijing and Lhasa.
One flight from Xining costs around 1700 incl. the permit, so I just heard.

One more word here to the Tibet permit:
It seems there is chances you can get the Tibet permit and could penetrate Tibet 'legally' coming from either Golmud or Chengdu, provided you get a group of around six togeher, who are willing to at least pass the checkpoints and it's towns around the 'border' as a group.
I have heard of three cycle travelers so far in Yunnan, Sichuan willing to share the path.
seb. in Korea, on the way to China