There are basically 3 variations for the arcade controller... most of the what has been posted I would say is the ONE variation... all that is different is some slight tweaking of the buttons used for x-ray and stuff. Here is my take on it. I only play on arcade and hitbox.
B = Block
S = Stance
I = Interact
T = Throw
The Standard Setup
1,2,T,I
3,4,B,S
This is probably the most common setup and so far is the one most recommended. There are tons of variations that resolve around moving the Block and Stance around for easy EX and XRAY. The main feature that combines them all is the standard attacks in 1,2,5,6 positions.
The 123 Setup
1,2,3,T
B,4,S,I
This is what I call the 123 setup. As "1,2,3" is always along the top and is the main feature. The goal of this setup is for super easy ex moves on all buttons by smashing with your thumb into the 5th position, probably the 2nd most easily accessible button on the stick. Like any setup there are tons of small variations with the other buttons.. a common one is to swap the "B" and the "4" around.
The Middle Block Setup
1,B,2,S
3,T,4,I
This is what I call the middle block. The basis set up is that the block in "in the middle" like the old school custom MK controller form the arcade days. Usually the variations revolve around the swapping the "B" and the "T", which in turn means you swap the stance for easy X-Ray. The idea here is that block is extremely easy to hit with all buttons using a simple two finger punch. No stretching your fingers like a piano player.
The Pinky Situation
1,2,S,B
3,4,T,I
The hitbox and its small buttons reduce the entire hand print size of the controller, it is way way smaller than the standard arcade print. This has opened a new setup that I have tried out and also seen used that capitalises on the smaller scale. The main feature here this time is the block in the 4th position, most commonly using the "standard layout" shown here... but works well with the "1,2,3 layout" as well. the idea here is that often when playing your pinky is kind of "up" and in a prime place to tap down on the 4th position and get a block in while you two finger punch, roll tap any other buttons you like. It works surprisingly well but feels odd at first, at least to me.