If you check your band, you will see that the maximum of your energy is of the order 1E-34 !
This means that you have a problem in your definitions.
First of all, do not define the Pauli matrices with hbar: You can see that your onsite potential is (as you defined it) t*hbar*sigma0. It should be t*sigma0.
For the spin orbit term, it depends how you define the constant alpha. if you check the reference , you will see that there is no hbar.
In your code, (after you eliminate hbar from the definition of the Pauli matrices), alpha becomes an energy, so you need to put a fraction of "t"
Check also the value of e_z and verify that it is consistent with the values of "t" and alpha.
I want just to stress that the transmission you are calculating is a number, so it will not depend on the change of units you did.
I hope this helps