I can see where you're coming from. I've never tried an Ultra or Elite so I really can't comment on those. I really haven't been keeping up with Fender's USA basses range, because as a lefty, I've simply never encountered one out in the wild to try! However, I do have some experience with their USA guitars, having owned a '00 American Standard Tele (from just before the introduction of the American Series) and currently own a '20 Mod Shop Jaguar and a '23 American Professional II Jazzmaster and I must admit: while they're silly expensive new compared to the prices of 25 years ago, they're a huge step up in terms of fit, finish and QC. My Jazzmaster does have a very obvious flaw that should'nt have slipped through (it has a flipped righty nut, so the top is angled in the wrong direction!) but the necks on the newer guitars feel amazingly smooth and everything else is just impeccable.
I won't compare the Jaguar as it is a bit of an oddball, and I suspect the neck for the lefty Jaguars involves more manual labour, because the Mod Shop and the Custom Shop are the only routes to get a lefty 24" scale neck from Fender USA (there hasn't been a factory lefty USA Jaguar since 1975).
Based on my experience with the Am Pro II Jazzmaster I don't really see the added value of the Ultra II over the Am Pro II aside from maybe the graphite rods in the neck and maybe the different electronics.