My car is due in 3 weeks, I went to have a pre-delivery chat with my dealer (Ridgeway/Marshall Oxford) to cover this and ICTP issues that I wanted to be looked at before I even collected the car. Their take on the shut line problem is that it's no better or worse than any other Jaguar model of recent times - a % of cars reach the delaer mis-aligned (and that % hasn't significantly changed), and they just fix it before the customer collection. They even showed my the history of my current Sportbrake which shows a panel misalignment that they corrected as PDI and recorded on their systems before I collected. What has changed is that most dealers are now selling 2-3x the number of cars that they used to
So if dealers aren't sorting this then I would guess it's because they're struggling to deal with the increased volumes of sales (and all the changes to the model ranges) with the F-type, XE, XF, and F-Pace. Most Jaguar dealerships have simply not seen this rate of model turnover or all the new tech that's coming into Jaguars and a lot I think are struggling to cope.
You only have to go back a couple of years to find they only sold 3 models (XF, XJ, and XK) that were frankly at least half a generation behind the latest cars of the day - now it's the XE, new XF, XJ revision, F-Pace, F-Type, and an XK in desperate need of a facelift. 5 of these models are basically new inside the last 3 years and use basic manufacturing and build technology that is light years ahead of what they used to be.
That's not an excuse for failing to deal with this sort of thing, but more an observation that picking your dealer at the moment is probably more important than it has ever been for Jaguar, and more important than it is for a brand like BMW, Lexus, or Mercedes, where this sort of model and technology turnover is old hat to them. You only need to look at the number of Jaguar dealerships that are currently in the process of building new showrooms (such as mine) or redeveloping (such as Guy Salmon in reading) to realise the upheaval that;' going on as the level investment involved in Jaguar dealerships changes drastically.