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If you want the ROM to have the exact same MD5 hash as the one listed on No-Intro all you have to do is to replace the header at the beginning of the file.
Replace these bytes:
4E 45 53 1A 10 10 50 40 00 00 00 00 00 00 00 00
With these bytes:
4E 45 53 1A 10 10 50 48 00 00 00 00 00 00 00 01
If you want to read more about the iNES and "NES 2.0" header formats you can do so here:
https://www.nesdev.org/wiki/INES
https://www.nesdev.org/wiki/NES_2.0
I kind of blame No-Intro here. Even their dump of the ROM from this Steam release has a modified header with the new format. This is weird since the actual ROM stored in the Steam release has the old header format. Additionally all ROMs of the game available online have the old header format.
First of all, let me answer why the checksums did not match up between the ROMs you dumped via my tools. The Python tool had a bug where the ROM was an overdump. Basically my tool wrote 400 additional bytes at the end of the file. That isn't really an issue for the functionality of the ROM but it is definitely a bug. I've went ahead and fixed that bug. The link in the guide already links to the updated Python code so you can go ahead and try it again. The ROMs should match now.
Second, the answer for why the No-Intro DB lists a different MD5. NES ROMs usually contain a 16 byte long header at the beginning of the file. This header contains information about what hardware the ROM requires so that emulators know how to emulate the game.
Likewise, via the RAM steps, the result is AD0D8625249774C6C819238F71A86C29. Why are all of these checksums different?
https://datomatic.no-intro.org/index.php?page=show_record&s=45&n=0857
⠀⠀⠀⣠⠴⠋⣡⠴⠛⠉⠙⠶⣌⡳⡆⢰⣚⡴⠞⠉⡉⠓⠮⣌⠓⠦⡄⠀⠀⠀
⠀⣠⠞⡁⠒⠉⠄⠂⢄⡡⣌⢠⠈⡙⢽⠷⠉⢁⡄⣡⡄⣁⠂⠌⠙⢂⠉⢷⣀⠀
⢰⠁⢂⠐⡈⠐⣈⡴⠋⠉⠈⠉⢳⡀⢸⡇⢨⠞⠉⠁⠈⠓⢬⡀⢁⠂⠌⡀⢉⠆
⢸⡈⢄⠂⠄⠡⣾⠁⠀⠀⠀⠀⠀⠑⠾⠳⠎⠀⠀⠀⠀⠀⠈⡷⠀⠌⡐⢠⠃⠆
⢸⢌⠢⣁⠊⠄⢿⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⠿⠀⢒⠈⢆⡌⠃
⢸⡌⠲⢄⠣⡈⠌⢷⡄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣠⡞⠃⡈⢆⠩⢆⡜⡁
⢸⡜⡱⢊⠴⡁⢆⠠⢉⠳⢤⡀⠀⠀⠀⠀⠀⠀⣀⠴⢊⠡⠀⢆⠱⣈⠇⡎⡴⡁
⢸⡜⡳⣭⢖⣡⢎⣐⣂⣄⠂⡉⠱⢦⣀⣀⡶⠋⢁⠂⣄⣂⣍⢦⡱⣬⢞⡼⣱⠁
⢸⣼⠋⠁⠀⠀⠀⠀⠉⠈⠛⠳⢆⣄⡻⣞⢠⡴⠞⠛⠉⠉⠀⠀⠀⠀⠉⠳⣇⡃
Anyways, even if they take this guide down the Github repository for the extraction tool should stay up.