IO540, can you elaborate a bit on your scenario? Within Europe, the only way you've got to show your papers to customs is either when entering the Schengen area from non-Schengen (that's the UK, for all practical purposes, considering the audience here), or vice versa.
The only way I see your scenario being a problem is when you fly UK to UK, with a fuel stop in France, or fly Schengen to Schengen, with a fuel stop in the UK. Not very likely scenarios, IMHO.
Or does this have something to do with the Channel islands? Have to admit I do not know their legal status exactly, and the availability/hassle of customs there.