Not knowing the certification background in detail for your particular aeroplane, I can only observe that the first segment data should relate to the post screen component of the gear retraction period (although one will see references to the first segment's being associated with post lift off flight). If your aircraft has been run through the process in the normal manner, then IGE considerations ought not to be of any significant concern for the first segment. However, the main consideration from a corporate risk management perspective is that a court case argument is going to revolve around what the AFM has to say so that remains the principal concern, I suggest.
The takeoff flare to screen is a fairly dynamic period but, whatever sums have been done during the certification workup, they will be validated by the FT workup.(often with a little bit of fudge factoring to suit getting the final numbers right for certification). As a general consideration, I would suggest that trying to analyse the detailed components of climb during the flare (in the absence of windtunnel or FT data) is probably a fairly difficult exercise and fraught with frustration.