While I prefer the auto-dimming mirror and the integrated Homelink garage door opener in my previous cars, it has not stopped me from purchasing a car without those features. I would never cross a car off my consideration list just because it lacked Homelink and/or an auto-dimming mirror because there might be other more compelling reasons to get that car. Now, if I had two equally compelling cars and one of them lacked Homelink/auto-dimming, then I probably would opt for the one that included it, or had it available as an option for a modest price.
I've owned cars where the Homelink buttons were active whether the car was on or off, and I've owned cars where it's only active when the key is present and the car is on. Go figure. Some auto manufacturers are a bit more security conscious, clearly. I haven't checked to see if the new Highlander Hybrid we recently got disables the buttons when the car is off.
I've been using the remote that came with the garage door opener in my Plug-in Prius. If I was concerned about someone breaking into my car to use it to gain access to the garage, I would simply put the remote in the center console, or otherwise hide in the car. Right now it lives on the driver's sunshade, like what many other people do. When I get the Bolt, I'll probably transfer the remote to the Bolt, or buy a replacement. I'd love to replace both garage doors to get the MyQ internet connected stuff, but I fear it's not really all that cost effective to do so and I think my wife would veto that expenditure.
The auto-dimming mirror is an available option on the LT, and comes standard on the Premier. Sadly it doesn't appear that Homelink is available. None of the order guides lists as an available or included option.