What is the logical difference between a "Call transaction using..." in ABAP and an InputScript?

There are 2 main differences between ABAP call transaction and InputScript:

- The InputScript remains active while you process the transaction.
In particular, you can read all screen values and make decisions based on these values. 
When you implement a Call Transaction in ABAP, you have to deliver all input data in advance.

- GuiXT offers a number of built-in features. For example, GuiXT will automatically display those popup screens that you do not handle in your InputScript, so that the user can continue, even in a situation that you did not anticipate.