The system bootloader is not really intended to be used in other way than through reset, so it probably assumes it can safely set GPIOs to reset values.
You can single-step the bootloader and observe, what does it do exactly.
Yes, but appnote is lack of info , and stepping consume time. Simply I see that all pins on portA is redefined, but portB stay untuched. Why not only used pins and why not documented ?
Which module is it? Does it support 9-bit transfers? If yes, you could then emulate the parity in the 9th bit; if not, well, the only option is to write a custom bootloader; if it won't fit, you have to migrate to a bigger mcu.
