I check-in at LHR where ever is easiest. I've checked in at a Y desk when flying F because it had no queue. When the delightful checker-in realised I was in F she explained there was a special F area and tried to send me to it, but I did not need to and all went well.
Last time I flew Y on IB I checked in at the F area as I was uncertain if I could check-in luggage very early for an IB flight. The helpful staff at the reception made a phone call to clarify and then I checked my bags in. Off I went to London for the day!