Update on my truck:
The dealership replaced the tailgate lock assembly on both sides. It's been about two weeks since the repair and haven't run into any issues so far.
I think I've seen a few Tacoma YouTubers talk about needing to get a mounting bracket for the front camera if you change out the grill. I'm not sure where from, but I bet a quick Google search will get you there.
I haven't heard of any solutions yet. I had the concern about my bed cover as well, but was able to get a video of it not working with the cover rolled up. I have my 5000 mile appointment on the 9th, so I'm going to ask them to take a look and make sure to show them this video.
It would make sense to me to change the functionality so when remote starting just don't search for devices to connect until the drive presses the ignition button.
I'll have to give this a shot. Especially since I have had issues even trying to manually connect to CarPlay, after remote start, that I just end up turning the truck off and back on again.
Has there been any final resolution on this issue? My '25 TRD-offroad started having this issue with under 1k miles on it. Haven't had the time to take it to the dealership yet, but hoping there's maybe a fix I could just do myself.