As part of a general cleanup to the UI of the Create Array...
tool, a new option has been added that automatically assigns the next available reference designator to the newly created footprints (it works in the same way as Paste Special... -> Assign unique reference designators
)
The cleanup was mainly to remove the clutter in that dialog when running from the board editor: none of the pad numbering options were relevant.

The way it should work is that if you have a block to array like below:
J1 J2
J3
It will create an array with the reference designators something like below (dependent on other footprints on the board not having those reference designators already)
J1 J2 J4 J5
J3 J6
J7 J8 J10 J11
J9 J12
A possible workflow for getting this working would be:
- Ensure that the schematic and the PCB are synchronised before starting.
- Use the array tool on a set of components of the PCB.
- In the schematic, copy the same block of components and do
Paste Special... -> Assign Unique reference designators
(they will need to be pasted as many times as required).
- Finally the components in the schematic and PCB can be linked up with a
Update PCB from Schematic... (F8)
selecting Re-link footprints to schematic symbols based on their reference designators
.
This option should be available in the next nightly run.
Ref commit: https://gitlab.com/kicad/code/kicad/-/commit/a79a2212573ab001402b01dcd2bf7a71ecc376cd