Deepak,
When they enter a SO or a Production order, the ATP works fine (allocates the MATERIAL A as per the requirement date / order entry date.
Sorry, but no, it doesn't. Except in MTO, ECC makes no linkage between the supply element and the requirement. During ATP, ECC makes a change to the requirement, creating a 'confirmed date and quantity'. It considers ALL supply elements configured in your scope of check. Any permanent linkage between a specific 'stock' element and a specific 'requirements' element only exists in your mind. There is no allocation of supply elements.
and that messes up the whole ATP which was performed earlier. The Stock confirmed for a Prod. Ord is reallocated to the SO (when V_V2) is run.
Well, if you mean that the V_V2 has caused overcommitment then it implies that your production order scope of check is not compatible with the sales order scope of check. You need to reexamine them to ensure that they are in harmony.
If you only mean that your CO09 screen elements are in a different sequence, then that is normal. SAP does not consider this to be 'messed up', that is the whole purpose of V_V2.
To answer your question; and as mentioned by expert Babu, GATP is more flexible than ECC when handling mass re-ATP of requirements. I will also say that if your goal is to consider fixed pegging (a hard relationship between specific supply and specific demand elements), GATP will support that requirement as well. Below is a configuration screen in APO
Best Regards,
DB49