If you apprehend that the builder may not be able to regularise the deviations hence will not be able to procure OC, your fears are natural and justified. You may issue notice in writing to the builder communicating your decision to cancel the booking in view of the blatant deviations made by him which would obstruct in getting OC for the building and unsafe to inhabit with a persisting fear of demolition by authorities due to the irregularities in construction deviating the approved plan.
If he is demanding the charges for the alterations made for your convenience, you may pay a justified amount from the demand, but do not commit in writing that you have agreed for the alterations and it was at your instance that the builder made the alterations in the flat, let this agreement be in oral alone.
After the legal notice, if the builder is trying to create problems on this you may drag him to consumer court seeking relief and remedy.