1. it is advisable to stick to in the DA or JV as to what is actually agreed between the parties
2. if a 41:59 ratio is agreed with 1900 sq.ft. coming to your share then mention that specifically. no need to separate the 1600 and 300 sq.ft as done by you in your query. the DA/JV must reflect the actual and true intention of the parties. what is important is that you should get in total 1900 sqft, now whether that much area is allotted to you in the form of 2 flats or 3 flats or whatever it is, would not matter.
3. once the DA/JV is executed and registered with the agreed area sharing ratio recorded in it, the builder would then have to submit building plans through his architect to the municipal corporation for sanction. Once the building plans are sanctioned, the parties can agree upon their respective flats in the new building to be constructed which would go to their share as per the area sharing ratio agreed in the DA and thereafter the parties can enter into a supplementary agreement to record the exact flats in the new building which will go to them
4. in my view the capital gains arise when the property is sold or transferred. By entering into a DA you are not selling your property. You are merely giving a license to the builder to enter on your land and do construction.
5. when the flats are ready the builder will have to register permanent accommodation agreement with the land owners to confer title on the owners. the flats would be of the area corresponding to the area agreed to be allotted to the owners. at that point of time the flats will have to be valued and the capital gains calculated accordingly. so instead of money you will get flats. now whether or not you are entitled to capital gains tax exemption is something which requires legal research. as per the prevalent law if capital gains from sale of property are invested to purchase a residential house then the capital gains are not charged to tax. however in this case instead of money the owner gets new flats. so whether he would get exemption from CGT is something which is not clear and requires extensive legal research
6. when the new flats are allotted under the PAAA to be registered in your favour by the builder, the stamp duty will be calculated on the market value of the new flats then prevailing (it is simple that you would definitely not know today what would be the market value of the flats in 2023 when the building is complete, also you need to factor in what happens when the construction is not complete within agreed period and you are allotted flats beyond 2023). however again since full duty would have been paid on the DA, it is to be seen whether the PAAA would attract any stamp duty if at all.