I think even if they cost more, it's still worthwhile if you're getting the gear ratio you want, a locker, diff cover, better shafts...a stock JK D44 that needs everything might not be such a good deal although JK owners who have a D30 would consider a stock D44 as a major upgrade.
Nothing wrong with Ford axles, they can be hard to find, sometimes they need a lot of expensive parts... hubs/spindles/gears etc plus all the usual upgrades.
My one other complaint with my particular D44 is that it has 76/77 Early Bronco knuckles on it... I love them because the steering arms are up higher than F150 knuckles, but I would be mega screwed if I ever break one. They are impossible to find by themselves.