Indeed that seems to be the case for various devices, even when the corresponding hardware in physically present but not available due to bonding/packaging, see e.g.
https://community.st.com/t5/stm32-mcus-products/rm0455-stm32h7a-b-reset-state-of-syscfg-pmcr-incorrect/td-p/178787
Most probably the reset settings of many (all?) registers related to bonding/packaging options are not fixed in hardware, but programmed into the mysterious 'engineering bytes' (along with calibration data) and copied into the corresponding registers upon reset.
But here it might be even fixed in hardware, as for this particular die apparently there is no package with PA15. Would be interesting to know whether register bits, output driver etc. related to PA15 are present and functional, i.e. what happens if PA15 is configured to output and toggled. Is output state reflected in IDR?
