Tom
From the Hawker manual re: second segment climb: "this extends from 35 feet to a height of 1500 feet or until the three and a half minute point is reached, whichever occurs first"
However, the manual also states "the charts in this sub-section (net take-off flight path) are provided to enable a complete net take-off flight path to be constructed........once it has been established beyond doubt that all obstacles will be cleared, there is no need to proceed further with the calculation."
That is what the manual for my aircraft says and 1500' is what my company and performance programme use for the end of the second segment regardless of clearing all known obstacles prior to that.
You really are getting your knickers in a twist over very little in my opinion. The time taken to 1500' with all engines operating is a matter of seconds in my type anyway so any potential unnecessary drag penalty by leaving 1st stage of flap set is there for such a short period of time as to be inconsequential. Maybe you should see if your type allows flap 0 take-offs; then you could rest easy.
Personally, I fly the profiles required by the AOC where specified and according to the flight manual and airmanship where not. What else can we do?
AP