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Isn’t a merged separation agreement better?

It may be, or it may not be, depending upon what you are trying to achieve. Agreements that are merged no longer have an independent life of their own. They cannot be sued upon as contracts; they may only be enforced as court orders. This may not be what you want. You may not want to give up the right to sue for breach of contract or "specific performance" (an order making someone comply to the terms of the contract). A merged separation agreement gives up this right.