There are different methods to use for each of focus trim, focus stacking and the hyperfocal tool. Given the flexibility of the XF there may be other ways but this is what I find myself doing:
Once set, focus trim is stored in the camera and automatically applied when the lens is mounted. The setting is linked to the serial number for blue ring lenses and to the lens model for non blue ring lenses.
Focus stack settings need to be specific to each capture and will be different for different compositions. Near, far and number of images are selected via the tools menu. I set near and far manually and in each case switch the lens to auto and save the setting via the top front and rear keys. Number of shots is set via the rear dial. Capture is started via the shutter icon on the top screen or via the rear user button.
Hyperfocal is set via the tools menu for each lens and invoked via the hyperfocal icon on the AF mode screen. To establish the setting for each lens, I spent a morning with the camera tethered and then shot to find a point where infinity was acceptably sharp at 100 or 200% in C1 on the pc. I then saved the setting on the camera. I used an aperture of f5.6 or so and normally shoot at f11 if possible so this gives a bit more depth. It's worth keeping a note of the number for the hyperfocal setting of each lens as it is easy to overwrite it if I'm careless.
If you take the lens off the AF mode switches from hyperfocal back to one of the other two AF modes. This also happens if you turn the camera off and turn it back on even without a change of lens. So although the hyperfocal settings are stored you need to make sure you have hyperfocal selected via the AF mode for it to work.
Apologies if this is teaching grandmother to suck eggs and as said above there may be other ways to do all this. I haven't so far used the HDR or time lapse tools.
Hope this is helpful.