Thanks for that reply.
I see others recommending to run auto-tune with the reactor/filter as well in that thread.
In contrast, while not the drive I'm using, this app note from Toshiba on auto-tuning drives for induction motors says the following: "The auto-tune will not work if there are other devices installed between the S15 and the motor like a load reactor, long lead filter, or sinewave filter. A manual tune is required, and is not covered here."
https://www.toshiba.com/tic/datafiles/app_notes/S15_App_Note_2.8.0_Motor_Auto_tuning.pdf
I'd assume from this that there is probably a preferred method regardless of drive used ...