I found a solution.
Change the line in startup.m to this:
set(groot,'defaultFigureCreateFcn',@(fig,~)addToolbarExplorationButtons(fig(~matlab.ui.internal.isUIFigure(fig))));
The function matlab.ui.internal.isUIFigure() test if the figure is a uifigure so this way it calls addToolbarExplorationButtons with a pointer to an empty figure if the test for a uifigure is true and to the desired figure if it is false.