If you run make menuconfig, deselect the ct driver and firmware package and select the original ath10k driver and firmware package, you will and up with these lines somewhere in your configuration:
# CONFIG_PACKAGE_ath10k-firmware-qca988x-ct is not set
# CONFIG_PACKAGE_kmod-ath10k-ct is not set
# CONFIG_PACKAGE_kmod-hwmon-core is not set
If you run ./scripts/diffconfig.sh > my_diffconfig, these will be preserved.
Note: At least on my platform the ath10k-ct driver depends on the kmod-hwmon-core package, while the default driver does not (nor does any of my other packages), so it's deselected as well. Depending on your hardware/configuration, you may still need the kmod-hwmon-core package.
In addition, you can also choose to build one of the firmware packages as a module that does not get included in the firmware image. That should avoid the error as well and gives you the option to manually install the other firmware package (using the opkg --force-overwrite option), so you can test the two firmwares against each other. In this case I would make sure to make a backup of the file /lib/firmware/ath10k/QCA99X0/hw2.0/board-2.bin though, as it will get deleted once you uninstall either of the two firmware packages.