See "montage_en_nf_b0.pdf" bundled in the v1.20 firmware zip file - page 3 mentions the control functions can be saved.

Touchscreen: Performance -> Motion Control (outside column of "buttons" on touchscreen) -> Overview (inside column) -> "Control Function" area.

Highlight "Elem/Op Control" and then save (store) the performance.

The v1.20 firmware should already have the "All 9 Bars!" performance, by default, with Elem/Op Control selected.

I do not have the updated firmware installed - but from the information it seems that it is likely to only save as controlling Elements from Part 1 and not allow saving also a pointer to a part other than part 1 for control. This is fine since you mention wanting the faders to control elements within part 1.

Assuming you have v1.20 loaded, from what you describe - getting the keyboard into Element/Operator mode for the faders does not change the selection of "Control Function" in the screenshot of page 3 in the new features PDF. Therefore, getting to this screen may be necessary to change the setting for saving. It's strange because the older firmware which does not have Element/Operator as a control function on this screen will still change between Performance and Part control and select (orange hilight) either Performance Control or Part Control automatically after pressing the same named buttons on the keyboard (no touchscreen editing necessary).

One way to get to the screen is press [PERFORMANCE] (HOME), then "Motion Control" -> "Overview" (although Overview is default for me without having to press it). Upper-right area is the "Control Function" area.

Certainly store the modified performance and name it something unique. I press [CATEGORY SEARCH] 3 times (or hold down [CATEGORY SEARCH] for 2+ seconds then let go and press [CATEGORY SEARCH] 2 more times) to get to user performances then the Part/[COMMON] button (button right under "[LIVE SET]") to select All - in order to call up my user performances.

I cannot confirm the functionality of saving a custom performance without updating firmware - but others have reported at least the presets which save the control function to Element/Operator do work correctly.

Circling back to the foldback:

Doing further research, it seems "All 9 Bars!" is in lock-step with the foldback characteristics of a B3 as documented here: http://electricdruid.net/technical-aspects-of-the-hammond-organ/

As long as the info on this page is correct - then Yamaha's implementation is also dead-on in terms of foldback.