I think it has something to do with several factors, some of those factors are based on stats, other are based on facts.
When passing through a birth chanel, a baby is exposed to complete vaginal microbiota of mother, and it is assumed that that first exposure to vaginal microbiota is the first of many factors needed for developing natural intestinal microbiota inside baby intestines.
For millions of years, humans evolved through natural vaginal birth.
As Fecal Transplant is all about attempting to return the clock and restore something to a 100% natural state.
We can only assume that birth alone also plays an important role in complete health, and also health of donors microbiota.
If you look at statistics, you can see that kids born through c-section have many times more health problems like allergies, eczema, etc ... in comparison to kids born by natural vaginal birth.
That is a first indication that c-section birth is not as healthy as a vaginal birth.
After a c-section, mothers are often treated with Antibiotics , to prevent infection.
Traces of those Antibiotics may end up in milk, and by that way may affect development of babies microbiota.
c-section in itself is a very advanced surgery that leaves mother in a lot of pain, sleepless nights. etc.
That will have negative effect on the quality of milk.
Mothers are also far more likely not to have enough milk after c-section.
Not having enough milk the first days after birth can have devastating effect on the development of microbiota and the development of intestines inside baby.
That first milk is what helps development of intestines, in terms of intestinal permeability and microbiota.
That first milk is there only for a few days.
But, if a donor is perfectly healthy individual, and the only problem is that he/she was born by c-section, I doubt it would be a bad dodnor.
I would rather choose a healthy donor born through c-section, a donor who has never been treated by Antibiotics , rather than choose another donor born by natural birth, but one who was treated by antibiotics at some point in life.