I have an ecosystem with miracle mud on my 40g setup. Macro growth has been awesome (probably due in part to high nitrates!). I have Caulerpa Racemosa & Caulerpa Nummularia in the refugium. (I have chaetomorpha in there also, but it isn't growing nearly as well). Everything in the main tank is doing really well, too (though it's only been set up for just under four months now).
I ended up adding a protein skimmer (CSS65) a couple of weeks ago due to excessive nitrates (20 ppm) despite regular water changes, etc.
Tests this morning revealed nitrates have dropped to 5 ppm.
My own personal experience is that I'm happy with the ecosystem set-up, but I think the addition of a protein skimmer (contrary to their recommendations) has helped my situation out immensely. At least, those are my early observations. Time will tell.