Most Home Assistant users would probably find it impractical to expose their hundreds of entities to HomeKit, (plus there’s a limit to the number of entities HomeKit can handle), therefore the include/exclude filters exist.
HA’s GUI has a GUI workflow for setting up the HomeKit integration but it is quite limited compared to what you can do in .yaml.
You can somehow limit down to domain and/or device, but there is no fine-control down to the entity level - no option to only include a particular entity and no way of setting configuration options for that entity (advertised name, switch as x, linked sensors, etc.).
Even more frustrating, if you choose to do a .yaml based setup, you’re stuck with it, so modifying an entity requires deleting the whole integration, editing .yaml then restarting, so it can be re-inited.
I think a way to re-use the .yaml config via the GUI would be the best of things - allowing more control to everybody while keeping the .yaml option for whoever needs it.