My initial guess is that there is a colorspace mismatch betwen the Maya viewer, and Nuke. Alpha values from Krakatoa can get to 1.0 with high enough density.
Can you run this simple test using Maya and Nuke (see attached image):
a) Render a Krakatoa image in Maya.
b) In Maya’s “Render View” window, select “Display”, then “Color Management”.
c) Question: What are the “Image Color Profile” and “Display Color Profile” settings? (see attached image)
d) Open Nuke, create a “Read” node with the resulting EXR file.
e) Question: What is the Read node’s “Colorspace” setting, and what is Nuke’s viewer’s colorspace setting? (see attached image)
The settings in Maya and Nuke must match otherwise the image will be interpreted differently. Is there a difference in the images when using matching colorspace settings?