Yes there are wheels in the middle of the locomotives, that it what allows them to follow tracks. So no, none of them are going to sit properly when not on the tracks. As for the second video, it looks like that BNSF SD60M might be too wide to fit properly into the rerailer track. I will take a look at that in a future update. For right now, I suggest you just rail the trains on regular straight track. There is not something wrong with the mod.