The WAT limit requirements are for still air and in isolation to other considerations - the relevant bit of 20.7.1B specifically cites no ground effect for the first segment. That is to say, WAT limits are just lines in the sand to give the aircraft an absolute basic level of performance so that we don't have to rely too much on the curvature of the earth ...
If you have an aircraft with a poor first segment then it is sensible risk management to keep the first segment not less than an upslope runway for obvious reasons.
When does the first segment present a problem ? - ie when are you likely to be through screen before the gear has had time to retract ? -
(a) when the performance is comparatively high - low gross weight, low Hp, low OAT. Conversely, for most aircraft, high gross, high Hp, high OAT and you generally don't see a first segment as the gear is up prior to screen. That is, for most aircraft, the runway slope isn't going to present too much of a concern.
(b) high wing, physically large aircraft with nacelle mounted gear which takes forever to retract. A good example is the AW650 Argosy (remember IPEC Aviation ?). The good old Queen of the Skies ALWAYS had a first segment for EVERY takeoff. For such aircraft, first segment is something to consider due to its not inconsiderable length over the runway.
Going back a little while, I looked after IPEC's performance on the AW650 and DC9. For the Argosy, we took a management decision and made it policy to limit the RTOW to achieve not less than runway upslope for the first segment. Lost a few kilos but everyone slept a little more peacefully at night ...