Yes, I think that this is complained about quite a lot, but the solution is very simple: call BA to book it, upgrading only the long-haul sectors.

The technical reason for this phenomenon is usually that if you try to do it online, the system sells you a Y, B or H fare for the short-haul sectors and combines it with a CW fare for the long-haul sectors so that you are then upgraded from ET to CE on the short-hauls and from CW to F on the long-hauls. The fares that can be combined like that are often eye-wateringly expensive, when actually what you are wanting to do is to buy a cheapo cheapo CW through-fare and only upgrade the long-haul sectors.

So the answer to your question is no, it is not a racket. It is just that (like with so much in life) you need to know what you are doing in order to get the best out of it.