I'll bite, and discuss it theoretically, although "good enough to great for the money" is their strongest real world selling point.
I would expect better materials and tolerances in tuners and bridges. And better consistency.
The tuners on both my basses are not very well fit where the ear joins the rest, causing rattles. The gears are solid enough, they hold tune, and nothing carries over the pickups, but I would expect better fit for $1000.
Bridges are not always great. My P bass bridge is fairly solid, but my Jazz bass has a lot of slack between the saddles, that cause the strings to move around and go in and out of alignment with the bottom of the neck and pickups. Nice, well fit steel bridges, with good saddles would be a mandatory.
On the Affinities, particularly, better pots and caps. With single coils, either Jazz or Precision, the 500k mini pots are a real weak point, IMO. I always found them to be noisy, have too much high end vs Fenders standard of full size, 250k pots, and be of limited use. Even if keeping the stock pickups, replacing the rest with Fender grade stuff has always made a huge difference, IME.
Better neck pocket dimension. Seems too deep on both mine. Maybe it's because they are older, or just my luck with these ones, as the newer ones I have tried don't seem so bad, right off the wall. But I had to shim both necks to raise them up a bit, as they seem too low in relation to the bridge. Getting low action dropped the bridge saddles so low the break angle was insufficient. Good breaks angles raised the action way too high.
It better come with a nice case.
So, to me, a $1000 Squier would have to be pretty much the equal of a comparable Fender, in just about every area.
Cheap Squiers work for me, precisely because of their low price. And because of that price, I accept that I will I have to do certain things to them where they are the most weak, and I enjoy doing it anyway.
It may still not be a huge amount of money, as instruments go, but for $1000, I would very much expect NOT to have to do those things.