It is just the hardware that is different. All still use SCT software and with a competent tuner, there will be no difference in the tunes themselves.
Picture the SCT handheld as a Windows based laptop. The X3 is say a Dell produced in 2005 and the X4 is say a newer Dell XPS. Both operate on the same updatable Windows operating system; however, the hardware (laptop or handheld itself) has been upgraded. SCT regularly offers software updates through their Device Updater program.
The X3 has less features than the X4, but for most purposes, will perform the same. I've had both. Avoid the BDX, as it often has connectivity issues with the 3v ECU and can present problems when datalogging.
I'd also recommend against just running the SCT factory canned tunes, or any canned tune for that matter. Consult someone reputable who will datalog and revise such as Lito. The majority of the tuning community uses either SCT software and hardware or HP Tuners. Most of the Ford Modular crowd has adopted SCT, so you will generally have more offerings there with tuners. If you start tuning yourself, HP seems to have a lot more capabilities, but SCT seems to have more base configurations for the Ford Modular offerings.
Best of luck to you, and I hope you enjoy the car.
2007 Mustang GT 302 stroker 6060 swap, 3.73 gears, Hidden Hitch Receiver, Barton Short Throw, JBA LTs, Borla Touring Axle Back, Lito tuned SCT X4. BMR SP009, Bilsteins, J&M CC plates, J&M LCAs. 4 Piston Brembos
DOB GT450 with VMP Gen II 2.3 TVS | 13/14 GT500 HE & IWP | GT500 hat & DW340s | FRPP 52lb | CMS Stage 2 Blower Cams | Comp 113 Springs & Retainers | 8 rib conversion | Track Spec GT500 Vents | PTFE Heat Barriers