The level acceleration phase will be carried out at a gross level acceleration height so far as the pilot is concerned, and he will be presented with that height. The engineer computes the obstacle clearance on the net acceleration height. eg for a simple example on the JAR25 Jetstream 41 the AFM states the pilot flies gross at 500 ft minimum, the engineer computes the obstacle clearance at 400 ft net. Hence a gross to net margin or safety margin is established in the AFM which on most other types will not be a fixed value, eg the 146 / RJ.
Surely that 1.2% gradient mentioned for the jungle jet is the minimum required 4th segment climb gradient as per JAR25, FAR25 ? (Not that I have first hand knowledge of that jet.)