With production leveling and sequencing/scheduling there is the possibility that you'll see and Automatic 2-door then a Manual 4-door or any possiblity in between. And if there is a issue on the line whether it be due to quality, material or an act of god it will shut the whole line down, which...
Have you seen this video?
Assembly is literally one line that snakes throughout the plant, it is literally is one car at a time down the line with both 2 and 4 doors.
They get painted in batches and then sit in a bank/selection area before they reach trim, this is why you will see different colors on the line. This helps with production leveling when it comes to building models with certain part limitations.
my alpine system I have in my 2020 willy's 2-door sounds great when compared to the harmon kardon I had in my alfa romeo giulia and the beats i had in my compass.
Do you have a soft top? What about the alpine system in your wrangler sucks?
Realistically all parts tend to be available it is the quantity that plays a factor, there are certain limitation due to production schedule and what suppliers are able to produce. These limitations will cause restrictions within each line of the plant which leads the plant to level production...
That literally makes no sense, if they are using OEM parts there is no reason why it would create any issues with your warranty... thats like saying that installing the Mopar sidesteps would void you warrenty. It sounds like the dealership is doing a run around with you...
If the dealership installed OEM parts correctly there should be no issue, if you are still getting a message it should be a red flag that they didn't install it properly. Just because they now "work" after several trips back to them doesn't mean that they are functioning properly as they should...