I think they charge on the basis of the highest of the co-terminals. I'm travelling much, much less these days so it's been a while since I had any sort of ticket using co-terminals, but not so long ago that the taxes were collected at the airport! Last time I did it would have been about 3 years ago when I had part of a DONE4 (issued by CX in Taipei) open-dated as LHR-WAS-NYC-HKG where what I ended up flying was LHR-BWI//IAD-EWR//JFK-HKG. This caused absolutely no problems at all at the time.

But now we have the "progress and convenience" of e-ticketing, which as far as I am concerned, as it is currently implemented, is actually all about the profits and convenience of the airlines and is a major step backwards for the customer.