Hi Batpig,
I'm a little confused (and probably missing your point) but what it the difference between setting the puddle flange into the slab, or setting it into the screed.
I've just started our bathroom reno and am using a waterproof membrane that sits on top of the screed and I just intend to set a puddle flange into the screed - level with the top of the screed. The waterproof membrane then goes down into the flange.