I've not seen any issues with HAP, HAPQ, or HAPA aside from some limitations on the final output and gradients, but that's unrelated to WO.
Usually for HAP I would look into how many cores you have available. I personally go about half that many as my chunk size.
My workflow however is just directly from after effects/premiere and export as HAP from Media Encoder and no converting from other codecs if possible.
I usually use 5-6 chunks and seem to have no playback issues. This plugin from GitHub hasn't given me any issue for Media Encoder, but now and then on ME updates I'll uninstall and reinstall it.
But I personally try and export the first export as any of the version of HAP I'm using with no converting in between