Atmospheric attenuation calculation for a 1550nm link budget
Unfortunately, no justification is provided for the "Clear air
  transmission loss" term, which is about 11km at 0.2dB/km, rather than
  483km.


Clear AIR transmission loss happens only in the lower layers of the atmosphere, which are the ones where the air is. That's where the 11 km figure comes from.

The troposphere contains 80% of the total mass of air of the whole atmosphere. The average height of the troposphere is 12 km, and ranges from 8 to 18 km depending on the latitude and the season of the year. I've seen 11 km being used in a lot of satcom link budgets, it's a pretty conventional value. 






  If the effect of atmospheric attenuation becomes negligible beyond a
  certain altitude, where would that be?


At the tropopause (the layer between the troposphere and the stratosphere). 



Image source: wikipedia article on Atmosphere of Earth.