Does the file size restriction include the environment that the game runs in? For example, if I targeted DOS or some other non-native platform, would the size of the emulator executable count towards the 1.44 MiB?

No. That's like saying the size of Windows or Mac is included in the game.

Cool, So if I submit a game designed for an 80's computer that could run in an emulator that would be ok?

I dont see a problem. If people can make games using the browser, Im sure there are no browsersunder 1.4MBs