don't get written to the output dotfile at any point.
However, the dot_options should be written to the file, see line 211.
It looks like the "normal" color could reasonably be patched in at line 282, although it would require some sort of mapping of color to hue.
The scale label is hardcoded in at line 366.
The flux is actually a log normalized ratio of the flux of a given path over the maximum flux over all paths, see for example line 254.
More generally, the ReactionPathDiagram isn't used too heavily as far as I'm aware, there is definitely room for improvements as you've found.
I would suggest the following; first if you wanted to add some of the features you needed directly to the C++ source (the python bindings that map this into C++ appear to be in place), a pull request on github would definitely be welcome.
However, in my experience getting a publication quality dot graph ready typically requires hand-styling no matter what you do.
Perhaps as an intermediate step, I would write a simple python script using regex that would read in the dot file and add/change the attributes you need (colors, label etc.).
I believe there are actually dot graph bindings for python as well, which may make your life easier.