I must admit I agree it is annoying. I wish there was a facility to treat it as APD exempt when you are on separate tickets but you are genuinely in transit with < 24 hours between flights.

On the other hand though I had a "weird" situation when flying on two separate tickets (it wasn't planned that way but due to my schedule change) on TK somewhere, I think it was SIN. When I requested to through check my bags, I was told that I had to pay £120 or whatever it was extra to do that. I was a bit shocked and queried why I was being charged for baggage. The staff were baffled too, but eventually tracked down what this was all about. As it turns out, the system said I had to pay the APD for SIN if I don't pick them up at IST and re-checked them.

It seems rather one-sided. If they charge me the APD on separate bookings going via somewhere, then I'd expect not to be charged the APD on separate bookings that effectively create a "connecting flight" situation.

Whether TK was correct or not, I am not sure, however. I collected my bags at IST as I had a long connection there anyway, so I did not pay the long haul APD.