When the UK ETA system is fully implemented (it was on a transitional phase — not sure if it still is or not), you won’t be able to check in online without an ETA, UK passport, or UK e-visa. I think a check-in agent at the airport can override it if you show them a physical visa, but those are supposed to be phased out by now too. I think this is all very similar to the Canadian ETA — I wasn’t able to check in online a couple of years ago until I replaced my UK passport with my Canadian one in my PNR.

Up until this year I usually just had my Canadian passport in my PNR and just used my UK one at the LHR immigration kiosks, but have now been putting my UK passport in for the outbound trip and replacing with my Canadian one for the return.