Intended the main Contractor will assist designer before build under an NEC3 ECC Option A. NEC3 ECI only appears to be applicable if contractor then engaged under an NEC3 ECC Options C and E?
Your question refers to NEC3 but I believe this must be a typo in that you mean NEC4 and the use of X22.
In principle yes you would be able to use the intention of X22 but not X22 itself. I would suggest you could recreate the process as Z clauses excluding those that relate to Option C and with careful consideration as to whether there will be an incentivisation against the Budget and how the Contractor will be reimbursed for its input in to Stage 1 and hence what provisions from X22.2 would be required. It would need careful drafting and checking.
You might find it easier to just have separate contracts - possibly a PSC Option A for the first stage (unless there are any advance works to do) and then move to ECC Option A for the construction phase.