How to Pad a File to a Desired Size Using dd Command

What dd reads when you run dd if=/dev/cdrom of=foo2.iso is not a file (there is no such thing on a physical CD), but a number of 4KB sectors. If the length of the image file you wrote is not an exact multiple of 4KB = 4096, there will be some padding at the end. You can safely ignore it.

You could use GNU coreutils head instead:

{
  head -c 16   > /dev/null
  head -c 1m   > PRGrom.bin
  head -c 512k > CHRgfx.bin
} < 'MMC5 EXAtt MegaMan3.nes'

(that's Unix shell syntax, you may need to adapt if using a Microsoft command-line interpreter).

You may want to consider cygwin instead of that ancient gnuwin32 on Windows which will give you something closer to a proper modern GNU-like environment (Linux is not an OS btw, just the kernel found in a few Unix-like and non-Unix-like OSes).

skip_bytes was added to GNU dd in 2012 (coreutils 8.16). The latest version of that gnuwin32 is from 2005 (though I suppose that's contemporary to your Windows XP). You can find compiled versions of modern versions of GNU coreutils including dd in Cygwin and Git for Windows at least, both of which also come with POSIX shell interpreters. Cygwin has stopped supporting Windows XP circa 2016, but you should still be able to download versions from around that time from there for instance. Git for Windows dropped support for Windows XP after version 2.10.0, but it's still available online, and both postdate the coretutils 8.16 release.