Hi William,
From reading your detailed outline the whole role definitions do sound quite confusing.
So my take on it is:
Manageallocations - gives the role holder the ability to assign specific users marking permissions on specific students
Managegrades - links to the dropdown you have posted, people with this role would be able to set the marking stage or phase
However, this is far from clear! - and I agree clarification on your last point would be useful. Perhaps log it as a tracker item to see if it can be explained.
All the best
Mark