The distance differences you mention are probably "as the crow flies" as was mentioned above. I'll pay closer attention when I plot a new route over a longer distance and see if that is the case. If the final number still is off after the route display is up, then maybe she took you the long way. Not being familiar with the highways you are reffering to, I can't comment on them, but as you'll see by my attempt to hijack your thread below, some of the routing decisions might be based on freeway vs highway vs roads and the fact that it treats them with slightly different priority because it will assume the travel speeds are different. But that wouldn't explain the different in "shorter route" mode.
I am actually having a similar "problems" if you can call it that, with my D3's navigation abilities. "The Lady in the Box" suggests I stick to certain freeways (big lines) rather than state highways(thinner red lines) which for all intents and purposes are essentially the same thing in Los Angeles. The problems I am running into are:
1) She refuses to stick to the route I've chosen (despite her giving me a different route) and will continually try to turn me around until I get far enough into the route where she suggests side streets to get to the other freeway (for those familiar with LA, I am referring to the 210 West of the 15, she'll try to take me down any of the N/S streets back to the 10fwy). This is a bigger problem for me as I tend to travel the same route to work and would like it to detour me only if there is traffic. (actually just tell me about it so I can adjust my route).
2) I can't seem to figure out the navtraffic detour and how it goes about figuring out a new route. She seems to get me off the freeway and try to get me around it, but I don't mind a huge detour if I can stick to higher speed roads. She managed to get me off the freeway in Watts (yes, SouthCentral LA) the other day as I wasn't paying attention. I was able to use the navtraffic tonight to my advantage, basically what I did was let her plot "her route" home and then I zoomed out on the map looking for traffic and accidents along the way. I managed to avoid one manually as it wasn't on her route, but the 2nd one she told me about and give me the option to go around it. Third one she warned me about, but I missed hitting the button, I got off the freeway and started heading in the direction of home (i was about 5 miles away) and she kept trying to take me back to the freeway which was almost at a stop due to construction traffic.
I've only had mine a week, so I guess there is a learning curve to these things, I do wish there was a way to manually plan a route and save it for later so I could use it to go back and forth to work. This would probably help the first poster in his long route setup. Overall I am really happy with the unit, there are just a few things that the manual doesn't cover at all or cover well enough to figure it out. Kinda hoping someone here has a few suggestions.
Again..sorry for hijacking your thread, but hopefully someone can take a stab at these questions and help us both.