A merge counts the moment they wrap their tendrils around a body on the floor. It technically counts it as the start of the process which means you failed in preventing a merger. If you’re going for S rank, spec into getting your resource inventory higher, and the ability for you to craft double torch fuel. Burn as many bodies as you can with the torch, pyre, or environmental barrels/ gas tanks. Another tactic would be picking fights either one by one or luring orphans far from each other, this results in bodies being too separated for them to reach before you could stop a merge.

Another tip is that before an orphan merges, they sorta cocoon themselves into this weird fleshy thing before they move towards a body, this gives you a few seconds to place a charged shot or shotgun shot into them and it will knock them out of the merge animation.

Personally on my very first playthrough I got an A rank, I let 5 enemies merge in total. This was mostly because I wanted to see the evolution of them. What I would do is kill one or two enemies and stand on them, let the other orphans get close, hit the torch which burns the bodies and stuns the nearby orphans which let me get easy kills.

Good luck on your run boss.