Yes, we do. It's all calculated using our Onboard Performance System...and we account for everything, including gear extention.
Of course, if the climb performance is in excess of the climb gradient required, then it's really irrelevant.
Whereas second segment performance begins with gear retraction and extends through typically 400-1,500' (depending on obstacles), if one hasn't retracted the gear and has first segment performance data, then one may use that. If one's performance is far in excess of the required gradient, and if one is using diverse criteria (you do know what that is, right??), then it's largely irrelevant.
You're so technical. "Messing with the numbers." Imagine what you'd say if you really knew what you were talking about!