Your #1 suggestion, I assume the JMP folks believe they are covering with the "General", "Styles" and "Fonts" preferences......If you have some more specific preferences that you see are common, that might make more of a case.
As far as you #2 suggestion, I completly agree with. If I can use a platform, to setup the display, just the way I want, why not just make a selection to move those settings to the preferences
for example i am making a variety of histograms. i need to customize each one to get the layout i want (horizontal, count axis on left, axis labels, no outlier boxplot). there should be a "set as default for this graph style" option in the right click menu