The Nav only makes minor adjustments based on your energy consumption and I believe it only makes adjustment based on the current drive, definitely not previous days. Your bike rack with two bikes on it is a relatively major modification. The Nav will not be able to adjust for something like that. If it were winter, you simply would have run out of charge driving that leg the way you did (following the Nav's advice on speed and slowing down to those speeds accordingly with complete disregard for the bike rack). Fortunately you had friendly weather.
I agree that it's unfortunate that the Nav often says "temporary closure" or something similar when in fact the supercharger is operating at a reduced service. Tesla has not been consistent with how those are labeled and there's currently no way to get real time info from HQ. I've run into this problem enough that I know to look at this forum and/or Plugshare to search for signs of life in these situation. In this case, with very little diversion, I would have stopped and checked on it regardless.
Lastly, I'd like to hear more about the a/c shutting off automatically. I do not own a Y, but I can't imagine that there is any way the car is designed that way. I have had A/C issues with my 2018 Model S (currently on my 3rd compressor and it's showing signs of failing again). I would be concerned that you too have a major problem if a new Y is shutting off the A/C automatically like that. Did you get any dashboard warning associated with the shutdown?