@LocoMatt you can manually convert project structure to match PlatformIO standards – see this topic. Or you can use my small Python3 utility to automate such process.
P.S. Actually, @ivankravets, can we somehow integrate this tool in PlatformIO CLI and/or IDE or give it a mention in docs? I don’t mean any self-promotion but people occasionally asks about CubeMX-PIO integration, so it might ease their work a little bit.