PF,
Afaik the route development funds from the Scottish Parliament (and NIA) didn't make any discrimination on airline nationality - I presume the EU would have something to say if they did?
The operation @EGO is more akin to a PSO, however artificially created this is! It is not as if Anglesey is floating in the middle of the Atlantic!
I would assume that any kind of regional fund would operate more like the former above, not the latter - but why taxpayer money is needed at all in a region with excellent (and now high speed) links to London is a mystery to me.
Having the government give with one hand and then take with APD (and take again on domestic routes) is even more daft! At least the Scottish PSO routes aren't subject to APD - it is of course so generous of the Scottish Parliament to hand out our cash to do this!