"If the alarm system wiring / fuse box is easily accessible through a popped hood that is a serious design flaw."
Well then, get thee to Detroit post haste, young engineer! There's (bad) work to be undone! Seriously, where do you think the battery is, does that need another door to protect that? What if the alarm system box is in the cabin? What then? Is there a place on a car, or a device that will thwart someone armed with manufacturer knowledge and devices, AND a properly fitted key? All they needed to do was disable the primary alarm, get in, program the new key to the car RFC/key thingy, and away they go! Which also answers your second question; yes they needed to disable the alarm, THEN they needed to pwn the engine electronics security. So, yes, they did need to "bother."
And so what. What if they just smashed and grabbed the car and hot wired it? Same thing, but not as elegant and effective as this method that a wacky Mexican biker gang (probably high as fuck on PCP, bathsalts, meth, and cat urine!) managed to do for several years without being nabbed. I say they did a fair job and a novel process. And nothing of value was lost! These are just shitty Jeeps, not the real Willy's Jeeps of old, just crappy SUVs barely suitable for a family outing, much less climbing hilly terrain. If you want a good off-road vehicle, get an old Toyota Land Cruiser, or a proper Indian(? or is that just the Jags?) built Range Rover, but not the Sport, or that Evomitch. Those are city SUVs, and strictly for the ladies.
"Are Jeep vehicles really wired that idiotically?"
Yes, and that's as good a job as they'll likely do. Take the most advanced car and security; it can be thwarted with knowledge of the system, and that you can get to the vehicle and physically pwn it. Here's a tip; park in a fucking garage. Most idiots just use the garage as another room of the house. It's for parking your car, if you would like it to remain safe throughout the night. Duh. I've yet to see a car that can't be broken into. Do let Detroit know of your special knowledge, I'm sure they will hire you straight away! :P