Seems to me FF might be the perfect solution to the growing to fast thing, instead of the whole restrict diet thing to prevent too rapid of growth. When I had a large breed dog, vet also told me lower protein feed was preferred to inhibit rapid growth that would cause problems later in life.
MANY feeds do have probiotic formulas already in them, like Purina flock raiser. Many that don't advertise it still have it. 

  If it's JUST the probiotics you are after, you could always do raw, unfilter ACV with mother in their water.
Even though I believe FF benefits ARE real... it's unfortunate that it tricks many of us into somehow believing that the prepared formulas aren't good enough for our birds. And if we give dry they are somehow doing with out, they AREN'T! They ARE formulated to meet ALL the needs of the fowl in captivity, assuming you buy the correct formulation for the species you are raising.
I do suspect your slightly runnier droppings to be related to the higher concentration of water in the diet. I would expect it to continue to level out over the next couple weeks as the feed change continues to take full effect. But like you say, runny is usually bad... good to keep an eye on things!
Like another poster mentioned, I would wonder if the bits you are seeing is just because the other stuff is more digested therefor making it easier to see what you currently are?
I think FF causes burbs... but I DON'T think it upsets the digestive system. 

 Yes, them are some pricey eggs your incubating. Totally a personal choice. Getting chicks to eat FF has NEVER been super easy for me. The ducks never thought twice before inhaling it. Don't know how an emu will react. If mixing it with dry makes you more comfortable, then by all means DO it. 

 Standard fresh INCUBATOR hatched chicks will ALWAYS go for dry and ignore the FF if given the choice, in MY experience. Like they don't recognize it as food. So it usually takes some tid bitting and encouragement/effort on my part to get them eating it... yes, stressed the whole time like they are gonna pass from nutritional deficiency from not eating the HIGHEST quality nutrients possible. 

 For those with broody mamas, they start just fine on it. Personal choice really, just don't beat yourself up about it whatever you choose. 
And thanks for continuing to share your experiences! 
I'm still not sure if having my ducks on FF is the right thing... they waste plenty of it slinging it everywhere, every time they shake their head. It was even higher than my head on the wall in my run! 

 And still lose plenty into the water dish. So I'm not sure for ducks how the savings will add up or not. But they seem to enjoy eating it and appear to be thriving at almost 7 weeks with NOTHING but FF and pasture. Since my flock is so variable with ages right now, I have no real numbers on duck FF consumption verses dry. And no previous experience with duck poo consistency/smell! 

  Kind of wish I did know the difference specifically for the ducks.
Keep us updated!