Development tools for Zephyr on STM32Workbench for Zephyr: VS Code extension to set up, build, flash and debug Zephyr applications on STM32.Devicetree manager: browse, edit and visualize Zephyr devicetree, STM32CubeMX-like for Zephyr.
The issue I describe above is only present if the "Generate Under Root" option in STMCubeMX is deselected.
So enabling that option is an easy workaround for the problem.