I’ve managed to create an image from master branch which is able to persist settings after reboot.
Select ext4 as target images, set 20MB kernel partition size, 100 MB rootfs size in menuconfig.
To flash fullimage (includes GPT, Preloader, ATF):
dd of=/dev/mmcblk0 bs=512 seek=0 if=openwrt-mediatek-mt7622-bpi_bananapi-r64-rootdisk-ext4-fullimage-emmc.img
To flash sysupgrade.bin (can also be used from luci, backup config works):
dd of=/dev/mmcblk0 bs=512 seek=4096 if=openwrt-mediatek-mt7622-bpi_bananapi-r64-rootdisk-ext4-sysupgrade-emmc.bin