I've read reports here of people doing just that- getting AA to have the one ticket "reference" the other (which, I believe, is close to the actual wording of the tax document) and have avoided the taxes. This is far from standard, but more than a few have reported it.
(I don't have time at present to find it, but I believe that these are in the main APD thread here on AA.)
Cheers.
Cross-referencing would be enough for the purpose of avoiding internal US tax on a US domestic ticket following or preceding an intl ticket but HMRC are rather more demanding with respect to APD: in addition to the cross-referencing, the tickets would have to be conjunction tickets, viz. tickets which are part of a single contract of carriage.
If both tickets are issued by AA and there are still coupons left on both tickets, AA could conceivably conjoin the tickets but this would have consequences on the contractual entitlements of the pax (notably shifting the risk of misconnect from the pax to the airline). If one of the tickets is not issued by AA, AA would not be able to conjoin the tickets. If both tickets were issued by AA but all the coupons on one of the tickets were already flown, it would probably technically constitute fraud, or at least tax evasion, to conjoin the tickets ex-post facto for the purpose of avoiding APD, although I doubt that HMRC would be that bothered unless it was a routine and systematic practice.
This does not mean that I do not believe that this has happened. I can quite believe that an AA ticketing agent familiar with US aviation tax rules but less familiar with UK APD might assume that cross-referencing would be enough to avoid APD.