I actually implemented pretty much the same layout (custom kernel, A/B partitions, but one each for the OS and the player software) for a similar use case (background music player). We used AUFS for partition layering. In particular, our setup was as such:
OS: SquashFS file system (ro) -> Config partition (ro/rw) -> tmpfs partition (rw)
Player software: SquashFS file system (ro) -> Data partition (ro/rw) -> tmpfs partition (rw)
The config partition is mounted read-only, all changes are written to the tmpfs partition. We then use a script to bulk write desired files to the Config partition (i.e. remount rw, copy files, remount ro). This limits the write time to a fraction of a second (these are only small text files).
As for the data partition, we remount the partition rw when we're updating the music files and check for filesystem consistency on bootup.
We hadn't had a single system fail because of the SD card in over 2 years.