Hi Shalabh,
You are correct that system will first split the costs according to target costs of the CE in actual price calculation. Details of this topic is explained in note 772794 which maybe you have already checked...
The cost splitting in actual price calculation is a 3-step process: split according to target costs/ splitting structure/ equivalence number.
So the splitting structure is only used when there is no target costs found on this CE and CE group assigned in target version.
Based on this, I can think of 2 direction of the solution:
1, make the target costs 0 so splitting structure can be used.
2, take another way around - make the target costs in accordance with the proportion of the SKFs.
Regards,
Sean