I asked on the hostapd mailing list and I finally got some help that helped me fix the issue. Basically, I assumed that I could do the same as with WPA2 and 802.11r where I could set ft_psk_generate_local to 1 and avoid having to deal with all the r0kh/r1kh parameters, but that's not possible with WPA3. The ft_psk_generate_local has no effect on FT-SAE. However, it's still simple to get things up and running: just set ft_psk_generate_local to 0 in the Luci interface and leave everything else blank. I made a quick test and it seems like the default settings enable my iPad to roam without issues between my two APs.
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