#2 is correct.
The calibration done in nanovna-saver is solely in the computer. It can't be saved to a slot in the nanovna, partly because -saver has more sweep-point options. You need to do the calibration on nanovna separately.
Also, it is important to note that (in ver. 0.4.0 and maybe others) the calibration done in nanovna-saver runs on top of the active calibration in the nanovna. [Some later version which I am not aware of may have a selection to use raw nanovna data.]
So it is important to save a basic broad calibration in nanovna slot 0, or a slot you will recall before each nanovna-saver calibration and use. Alternatively always reset or disable nanovna calibration while using nanovna-saver. [But sometimes -saver will get an error with the latter approach, due to out-of -range data from nanovna.]