mate, this is applicable for just about every airline out there. It's airline economics. Definitely not applicable just to Cathay - most airlines globally behave like this - and the dynamic has been around as long as I can remember.

The related concepts are point of sale (and, by extension, inconvenient routings) and economic price discrimination. For example, on the ZRH-BKK route Cathay is competing with a non-stop Thai Airways flight ZRH-BKK. Passengers choosing Cathay on that routing will need to take extra sectors and more time to get to their final destination. To further incentivize passengers, CX might throw in goodies like generous cancellation / change fees, "stopovers" (allowed to disembark in HK for an extended period of time) en route to the final destination, and other benefits.

A glaring example of this are Cathay's ex-Taipei business class fares to North America. They aren't quite as cheap as they once were, but you can still reliably get to North American destinations for <$4k USD by starting your trip in TPE (say, TPE-HKG-JFK-HKG-TPE) instead if Hong Kong, where you could pay as much as $7-10k USD for HKG-JFK-HKG. By the same token, CX is competing ex-Taipei with BR and CI who have nonstops to many North American destinations.

Then you have price discrimination. Business passengers ex-HKG (and also passengers with Hong Kong as their likely final destination) is perhaps the densest cluster of high-spending travelers in the world. Not the most - HK is simply not that big - but the average business traveler with business in HK has a greater willingness to pay for tickets regardless of the price (aka, prices of HKG origin/destination business tickets tend to be more inelastic than can be said for most other global cities). And so going back to the point of sale concept, the other fact travelers in Taiwan will need to pay a cheaper price to fly CX to N. America (other than the inconvenient routing backtracking to HKG) is because Taiwan has a lower GDP per capita than Hong Kong, is not the financial hub of Asia, etc. There aren't as many customers willing to pay HKG-style prices in Taipei. These factors are overwhelmingly true to the two destinations you mention, BKK and KUL.

To top it off, you have what's effectively a CX monopoly on passenger traffic at HKG, between CX and their subsidiary KA. HKG is their hub. There is a captive audience of frequent travelers who CX knows will prefer CX due to corporate policy, membership loyalty, etc. CX can, frankly speaking, charge this cohort more and they will pay up. So to sum it all up, by inputting BKK, or KUL, or somewhere else as your final destination, chances are the average traveler going to those places are more price sensitive, and they might have other more convenient choices to boot.