Fly Through. You may well be right about this being a negotiating tactic - it wouldn't be the first time! As for FR's costs increasing if they decamped to GLA, well that would depend on the deal they might extract from that airport. Rumour has it that FR have a good deal at EDI, at least for those routes where they are the only carrier (to avoid accusations of discrimination). If FR can do a similar deal with GLA then their costs mightn't increase as much as you would imagine, and it's possible they could recoup this through higher yields ex-GLA as compared with PIK.
Seafire6b. I think you are spot on about the future of APD. I think the attempts to tweak it are bound to fail. The only long term solution is to recharacterise it as some kind of environmental/congestion charge and apply it only at airports with excess demand and high environmental costs (ie Heathrow).