You'll actually get a lower climb rate with more flap but a shorter takeoff run
Yes I did notice the flaps were retracted from CONF 3 to CONF 2 when the gear had gone up presumably to increase the climb and speed.
When looking at the performance they may well have planned on full length, or at least a longer intersection departure using conf 2 and certain V speeds, but also looked up figures for a shorter intersection with flap 3 and written those numbers down . Once they have been checked by both pilots if you do get the shorter intersection it doesn't take long to change the performance page in the MCDU and select the correct flap.
I see, this does make complete sense now. Thanks for clearing this question up mcdhu, ATCast, Lord Spandex Masher and HPbleed really appreciate it
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