As far as the starting point check, i'm not sure what it would check, as you could click on the blue or green warp/start squares are to see where link would go--but i suppose it may be a good idea...
Yes, it would check to see if (Either, perhaps, of) the start positions are in the upper left corner, that they both default to. If they are, you might get a notification of some sort.
And all of these checks would be good regardless of whether or not such "mistakes" can actually be something done intentionally--i mean, take a look at the "show misaligns" for example--it'll show misalignments that are often times, in fact, intentional--such as water (which counts as a solid) being on the edge of one screen & the next combo on the next screen may be land but it'll still count as a misalignment.
Well, how often is it that you'll find a start position in the default upper left corner? And even if there is, then you can just skip over correcting that screen. No biggie. :)