Depends… To find out what is going on, it would help if you wrote down which steps you performed. Tools like reform-boot-config print this message when they complete:
Your /boot partition is on your SD-Card (/dev/mmcblk0p1)
Did you find a utility from which this information is missing? This information will not be documented in the manual as this behaviour is specific to A311D. The “problem” with the banana pi is, that if you would write a broken u-boot onto eMMC, your system will become unbootable and thus you would not be able to write a working u-boot to eMMC, thus soft-bricking your board. Thus, tools like reform-boot-config take care not to write to your eMMC if you are on A311D.
What program are you running and what error message do you get? The mntre.com Debian repositories are unsigned and this is reflected in the default apt sources. Thus you should not get a message about incorrect signatures. How can I reproduce the problem you see?