It is still working as Forms 9.2.  Deprecated means this option will only be available for save to repository service task upgraded from previous version and if you select other option and save, this option will not be available.

The only difference between the 2nd option(Save a form with current process data) and 3rd option(Save data from last submission (Deprecated)) is for value of variable used in the field settings such as Text above field/Text below field/Tooltip: when use 3rd option, the value for variable used in field settings is the value of the variable before the last submission step that is before the save to repository task(use workflow to change variable data is treat as a submission step as well); when use the 2nd option, the value is always the latest one.

Following is the example:

The three save to repository tasks save form 2 with different options: In form 2, a field use a field variable from form 1 in the text above field setting.

 In the start step, the value filled for the field is 1;

 In the task 2,the value for the field is changed to 2;

 In the task 3,the value for the field is changed to 3. 

For the form 2 saved with the 2nd option: the value in the text above field is the latest value of this variable which is 3;

For the form 2 saved with the 3rd option: the value in the text above field is the value of the variable before perform user task 3 which is 2.

The  behavior of the 3rd option for variable used in field settings is not very intuitive for user to understand and that's why we deprecate it. But if you don't care about variable used in field settings, you can continue to use the 3rd option.