It seems like I resolved the problem with devcube tool 1.0.9
you need to change f.ex. C:\IoT\Bouffalo\bouffalo_sdk\examples\peripherals\gpio\gpio_input_output\flash_prog_cfg.ini
[FW]
filedir = ./build/build_out/pwm*$(CHIPNAME)__d0.bin
address = 0x100000
After that blink worked on both D0 and M0 - haven't tried LP yet