I found this route too...
http://www.cycleontario.ca/pcrn/maps...ooToronto.html

It looks like it is trying to use one of the few diagonal segments of road between toronto and guelph
It goes through the north of the city instead of hamilton.

The one thing I noticed about highways 5,6,8,25 --- roos, is that in google earth, they are one of the few roads that appear at a fair zoom out, so perhaps it makes a good rule of thumb to plan a route using roads that only show up at closer zoom levels.

google earth is well worth the download if you plan to study routes between places. Better faster interface, and altitude info.

Are there any rules of thumb that determines the difference between country road and side road?

Are you recommending the trail because it makes for a charming/enjoyable journey, and country roads in the area can still be pretty hectic and nerve racking? -- so its not worth the shortcuts?