As you are mentioning the full Schedule of Cost Components, I will assume that you are working under one of the cost-based options i.e. main payment options C, D or E.
To see whether they are a Subcontractor, you have to look at the definition of a Subcontractor under clause 11.2 (17) and if they are, then the provisions of clause 26 apply including submitting the name of the proposed Subcontractor to Project Manager for acceptance (clause 26.2); being ‘encouraged’ (by the wording of the NEC) to use an NEC3 form (clause 26.3); and submitting the proposed Contract Data to the Project Manager for acceptance (option C, D & E clause 26.4).
So going back to clause 26.3, a purchase order is a contract, so those terms should be submitted to the PM for acceptance etc… A purchase order will typically by on Priced basis, so I will assume that whether it is a Purchase Order or an NEC3 contract, the sister company is paid for on the basis of prices tendered as opposed to open book Defined Cost. So for non-CE work in the subcontract, they will be paid for on that basis.
For compensation events, the main Contractor is still paid Defined Cost and the decision point you come to BEFORE you start looking at the SOCC is whether, under clause 11.2 23), they are Subcontractor or not. From what you have said, they are, so would be paid in accordance with that subcontract.
I have made a few assumptions based on what you said in this answer, so do not if they are wrong, then my conclusion might be wrong.