I noticed that the Ford Focus Wagon's have their own separate model names. Shouldn't the Ford Escort and the Ford Taurus have these separations as well instead of putting in the extra info?

Taurus Brochure's seem to list the wagon as separate but they have a trim/model name in front of it like MT5, SE, or SEL
1986 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_1986.pdf
2002 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_2002.pdf
2005 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_2005.pdf
1996 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_1996.pdf
1998 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_1998.pdf
1992 - http://www.auto-brochures.com/makes/Ford/Taurus/Ford_US%20Taurus_1992.pdf

The same thing with the Escort but it uses LX instead.
1992 - http://www.auto-brochures.com/makes/Ford/Escort/Ford_US%20Escort_1992.pdf
1995 - http://www.auto-brochures.com/makes/Ford/Escort/Ford_US%20Escort_1995.pdf
1997 - http://www.auto-brochures.com/makes/Ford/Escort/Ford_US%20Escort_1997.pdf

I personally feel it would be easier to make the Wagon's as part of the model name and then put the trim level in extra info. Thoughts

If it was used commercially in the name, indeed that could go in the model name.
But here even if they list it after the sedan, the "Wagon" part seems less important than the trim, so not really in the model name.