As I read it I think the OP is aware of that, I think the question being asked is what do you do with the numbers having extracted them from the CDL..
FWIW our 777 DDG/ CDL is surprisingly silent on this issue but I was taught to consider adding en-route penalties (temporarily) to the ZFW in the FMC if you are being asked to climb, the CDL penalties are significant and you are getting close the edge of the envelope
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