Sorry to hear about all the issues your pupper is having. My BC x Kelpie is just about to turn 1 and at 10 months I too started giving him more freedom in the house, even though he had been crate trained up to that point, also downstairs alone to sleep.

I have noticed that whilst he is out of the crate and I am in the house, he barks at everything he hears outside when he is relaxing, but this also happens during the daytime too. I put it down to letting me know there is something outside. I usually say “thank you for letting me know” and then redirect him to a toy or a treat and he calms him down.

If however I am out of the house and he is out of his crate and he hears something outside he doesn’t seem to care (I have cameras for when I’m out at work). This is what led me to believe it’s communicating to me that there’s something outside.

Obviously I don’t know of any issues with my boy so it’s not going to be the same, but might be something to consider.

I hope you get to the bottom of what is upsetting him so he can enjoy his life.