As per the referred provisions of the law which is given below:
(4) Where no objection is filed, the Tribunal may, after such verification
as it considers necessary, by order either grant or reject the application.
(5) Where an objection is filed disputing the validity of the applicant’s
claim or setting up a rival claim, the Tribunal shall, after enquiry, determine,
by order, the person entitled to be registered as occupant and pass orders
[(5A) Where there is no objection in respect of any part of the claim, the
Tribunal may at once pass orders granting the application as regards that
part and proceed separately in respect of the other part objected to.
Thus in case there is a claim by any person at a later stage giving objections to the same, i.e., if the builder did not obtain permission under section 48A KLR, then this problem may arise, but you can decide based on the prevailing circumstances in this regard.