The file system and security model differences are much more important than any terminal differences. Looking through the programs included in coreutils, I can see only two or three that care about the terminal at all (`stty`, `nohup`, ls output coloring).

I think "terminal" here also includes differences in the shell. For example if you type "command *", a Unix shell will expand the star before calling the command. On Windows the star is passed to the command.

not the mention the way disks, processes (unix forks and execs, windows spawns) and I/O work

And character sets. A lot of poorly-done ports of Unix software cannot cope with Unicode on Windows.