To repeat the answers you got at your cross-post https://stackoverflow.com/questions/69292456/logistic-growth-curve-using-scipy-is-not-quite-right
The logistic curve is rather rigid in its symmetry. Forcing the initial value to be some prescribed constant effectively removes a degree of freedom in the family of curves that are available to the fitting ...
I'm not sure if Nick's answer is right or maybe it was working in the previous version but it does not really in this one.
First of all, reverse_cuthill_mckee does not take a NumPy array as an input but it takes a csr_matrix.
I think it should be:
arr = [
[0, 1 , 2, 0],
[0, 0, 0, 1],
[2, 0, 0, 3],
[0, 0, 0, 0]
graph = csr_matrix(...