A lot of factors cause different dive depths. Angle the bait runs in the water is a key one. I would guess that the extra hardware on the jointed changes the angle. This why Precision Trolling Data is so important - you don’t have to figure out why, just pick a depth and let out the right amount of line.
Snap weight gets added at 50 feet line out. You will see "50 SW" on the PTD app under line out. That 50 foot leader stays the same for all depth and baits. See this animation for visual ru-vid.com/video/%D0%B2%D0%B8%D0%B4%D0%B5%D0%BE-nsXnGtALgoY.html
There are some baits on the app that have snap weight data. The app uses the 50+2 method. That means you let out 50 feet of line add your snap weight then let out more line to achieve your target depth. The app gives you total line out so that includes the 50 feet of line before the snap weight. Remember your speed greatly affects the depth of the snap weight so be sure to select the right speed on the app.