So did you succeed in overwriting the selection of the Hiragino font, or not?
Then, what does Graphviz specify, and where? I’m not accustomed to the code… (I might try to get! But it would certainly take time. The closest I can find is DEFAULT_FONTNAME · Search · GitLab)
One thing came to my mind to clear the picture, to do (in Bash)
for string in Times-Roman TimesRoman 'Times Roman'
do fc-match "$string"
done
It gives
NimbusRoman-Regular.otf: "Nimbus Roman" "Regular"
DejaVuSans.ttf: "DejaVu Sans" "Book"
DejaVuSans.ttf: "DejaVu Sans" "Book"
which is different both from fc-match serif (DejaVu), Graphviz without fontname (DejaVu), and Graphviz with fontname (EB Garamond). But really, I don’t know which one I should expect to be the closest match.