Doesn't really matter whether the drain plug is at the lowest level or not. You have to drop the pan to change the trans filter, and that's part of doing the job right. Another quart or so of fluid comes splashing out when the filter is removed, so this is the only way to change it all.
My understanding is that diesels don't like the crankshaft turned backwards. I *think* it's the injection pump which gets very unhappy - can't recall for certain.
I've never been able to line up the drain plug by bumping the starter either - and I tried using a remote starter from under the car! Had to break out the old 27mm socket and do it the manual way. No big deal - just wait for the compression to bleed down past the rings.