Is this a general thing? Is it generally better when buying a new car to go with the standard sound system and upgrade with after-market equipment?
Ehh, not necessarily. My Ford Flex has the premium sound system and I don't think I'll ever make a single change to it. For that vehicle, "good" is good enough.
For any serious audiophile, if you go into a purchase KNOWING you're going aftermarket eventually, it's usually better to go with the standard system and build it your own way. Otherwise you're paying for upgraded components that you're going to throw away. Because the standard systems are basically never as high quality as high-end aftermarket components, but you pay a premium buying it.
It's like the difference between a turnkey house and a fixer upper. Turnkey is great if you don't plan on changing things. If you find a turnkey house and it's got acceptable finishings, even if they're not perfect, and you're not going to change it, turnkey is easy. If you know that you're really particular and you have a unique vision for how a house should come together, a fixer upper is often better because your acquisition cost is lower and you're not just wasting money on the last owner's upgrades which you're going to throw away.
I think I know how Jeep got there, of course. They started specifying a premium audio package that could be as common across multiple vehicle lines as possible. I neglected to mention that the stock amp isn't just an amp, it's a sound processor. So my guess is that by standardizing on a head unit across multiple vehicles, and an amp/sound processor across multiple vehicles, they have commonality of parts supply and they can just program the sound processor for each vehicle based on its configuration. Maybe the other vehicles really make better use of an 8-channel amp, in a fully enclosed SUV, and sound great, and they shoe-horned it into the Wrangler. I doubt that the design was, from the start, Wrangler-specific. I think if it was, they'd have done things differently.
My Jeep was bought to be a daily driver. I never intended to upgrade the stereo, and frankly the job got away from me lol... It was only when I replaced the head unit, which I had to do because 2009 head units didn't have Bluetooth, that I started to go down the rabbit hole and see how inadequate the stock system was.
But what I ended up with was a system that's higher-end than stock, that was picked specifically to meet my likes, dislikes, and budget.