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I would seriously doubt that the garage door opener is causing the problem as it's on an entirely different frequency.    From your description, it sounds (to me at least) that your liftgate/trunk module (LTM) is failing. Its located inside the interior panel, just in back or the drivers rear tirewell. About the only common point common to all your problems. 

I'd start by checking the fluid level in the transmission. But usually tranny sounds are more like gurgling, grinding and whining.    It really sounds like a belt or pulley, possibly a belt tensioner (although you would think that the sound would also be present when switching to any other gear).   I remember reading in the Subaru forum that they had a similar chirping when cold. It was traced to the rear output bearing on the transmission. (Do you have an extended warranty)? 

Cut myself twice on that sharp edge!

Consider buying the Console Vault for your firearm.  Much safer from theft than the glovebox.  Lincoln matched the manufactures price and easy to install.  https://www.consolevault.com/console-vault.html?gclid=EAIaIQobChMI18OK7u-46gIVmv_jBx21ZwA_EAAYASAAEgIdHvD_BwE  

Had the same issue except the hatch wasn't fully closing, seemed to be but was was always trying to draw the hatch closed and eventually ran the battery down.  Didn't happen each time but after 3 jump starts in 2 weeks the dealer found the latch actuator motor was intermitantly bad and replaced it.  Appeared at 33k miles.  2016 MKX.  Interesting they replaced your motor and sensor with no result.

I only hear it once when I am parked and then move the shift lever from park to reverse.  It certainly isn't the brake wear indicator.  And actually, the chirping is affected by the pressure I apply to the brake pedal as I shift from park to reverse.  The harder I press on the pedal the louder the chirping.  So maybe it is some sort of indication th brake fluid is low perhaps?  By the way, I did clean off the backup sensors and tat didn't change anything.    

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