Your builder is making false claims. hence you can choose to ignore his claim.
Once the property is registered, then you have become the owner and also have the possession of the property.
However you are liable to pay maintenance charges from registration date till today since yours is a flat(maintenance comprise of common electricity, water, cleaning of common areas security etc).
There is nothing called Holding charges and your builder is claiming money under fictitious head.
Also in law, there is no provision for Separate Possession agreement after the registration of the property. Hence the claim of the builder for handing over of possession to you is a false and fictitious claim.
The duties of the builder includes the following in addition to registration:
a) builder should get the electricity , water and property tax records mutated in your name .
b) the builder should provide you the copy of the occupancy certificate issued by the municipal authority for the entire apartment complex. .
c) Builder should complete all the amenities in common area and hand it over to the flat owner's association.
hope this helps.