So, this isn't anything groundbreaking but it didn't occur to me until today so I figured that I can't be the only one.
Until this clicked earlier, I would either set a complete circuit coaster in shuttle mode, use the full manual controls, or make a really awkward connection in order to give it a run through to check for pacing or Gs in extreme seats etc. This definitely isn't ideal (especially using shuttle mode) because often the brakes don't work the right way. Connecting the coaster before it's finished isn't great in NL2 because now it screws with the banking and sometimes the shaping as well.
Well, the easy work around is to simply put a short block brake at the very end of the track before freezing. The coaster will then work in automatic mode in the editor, although you'll still get a pop-up message as the train approaches the next-to-last block warning of a Deadlock situation. However, this method will allow the train to run to the end of the track without incident and without any extra finagling.
I hope that helps someone, but maybe I'm the one late on the uptake...[confused]