I was just shown by a colleague that changing the Bubble Plot Color Theme IS possible (JMP 13.2.1) - it's just inconsistent with how Graph Builder works. In Graph Builder, you can double-click the legend and change the Color Theme from that dialog. Doing to in Bubble Plot leads to an inconsistent dialog without access to the Color Theme. However, access is provided through Bubble Plot's Red Triangle menu (provided an ID variable exists and displays as a legend). This was a huge relief for me, as I needed a gradient color scheme instead of the default diverging one for my situation.
So, it appears the feature request has been granted! A modified feature request would be to upgrade Bubble Plot's Legend menu to function more consistently with Graph Builder.