As I always advise everyone who wish to buy immovable assets involving huge investments, it will always be better to spend a few thousands on legal opinion from a local experienced and prudent lawyer who is knowledgeable in the property related issues. Now to your query
1) Is it safe to buy property which is under BDA and not BBMP ?
The khatha issue will have to be solved whether the property comes under BDA or BBMP before purchasing, have a confirmation about the khata. There is nothing wrong in purchasing a property falling within BDA
2) Does obtaining OC means that builder has complied to the corporation sanctioned plan and does not have any deviation ?
The authorities are supposed to sanction the OC only after confirming the construction in accordance with the permitted rules, so once OC obtained there is no question of worrying about the deviation, it has already been taken care of.
3) As per the land documents, it is a property which has multiple land owners and the same has been handed over to builder through a registered agreement and partition deed. Is it safe to buy such property ?
The documents are to be seen for giving proper opinion,you may refer to my introductory remarks in this thread.