.........the NET CEILING as explained in regulations, should be clearing the most demanding or critical combination. If it is not clearing, then either Take off weight (payload) should be reduced or an escape route should be planned. As seen, this is a very complex calculation. Additionally, if there is also an MEL penalty which is reducing this net ceiling, the calculation becomes even more difficult and only be figured out by a computer calculation. Besides, as AIB Pilot, there is no tool, software, charts or tables in our hand to do all these calculations.
Therefore, I believe all these calculation (including MEL penalties to NET CEILING) are done (or should be done) by service provider of Computer Flight Plan (LIDO, JEPPESEN etc).
Surely the point of the CDL penalty is that you start with normal planning and then simply apply the weight and fuel penalty. That does not need a computer, even though it will be done on one. The penalty is crude and conservative, therefore the penalised aircraft will in reality perform better but less efficiently than one dispatched at normal weight/configuration.
8che has a point. As a function of weight your aircraft with its missing part has more drag than is accounted for in the performance data. The FMC will overestimate your ceiling, and underestimate fuel burn. If you give the FMC an 'assumed' ZFW equal to the actual weight plus penalty, then the ceiling and fuel burn data will become conservative (you will actually do better). But there is a problem because the same is not true for driftdown speed. As the FMC now thinks the aircraft is heavier than it actually is, the computed engine out speed will be too high. Therefore the drifdown speed used should be that which the FMC would compute for your actual weight or which you would get from the tables. Even that will not be perfect because it does not account for the extra zero lift drag of the deviation, but I assume that the weight penalty is sufficiently conservative to allow for it.