I’ve had a situation where I wanted one render layer for a scene to have “render transparent“ turned on, but other layers of the same scene to have it turned off. Usually, this occurred where I wanted to composite a special render layer over the main one, and I needed the world background. In short, is there an easy way to do this? Compositing tricks are welcome, As long as they’re versatile. I have a pretty wide range of background types that I use.
This answer deals with the specific case of wanting two layers, but you would need to modify it to work for transparency. Transparency is a scene level property, so you would have to duplicate your scene, having transparency on in one and off in the other. Instead of just changing the Render Layer in the Render Layers node, you would also have to change the scene. And, of course, you'd have to render two scenes.