OK that all works. But on a pedantic point, you were claiming specifically that running through City Centres slows down the journey times. That's not quite what your Brussels-Amsterdam example shows - because - if you are correct - the slower journey times on that route aren't caused specifically by running through city centres, they are caused by using classic lines instead of building a brand new high speed line the whole way.
I think the correct statement is that, new high speed lines tend not to be built through city centres because to do so while maintaining the high speeds would involve huge extra expense (because of the tunnelling and underground stations you'd probably need). So they tend to serve intermediate cities by spurs because it's cheaper to build. I would argue that, if the money for the extra tunnelling could be found, then in principle it would be better to tunnel the high speed lines to serve the city centres because then you can run a more frequent turn-up-and-go service (for example, running London-Birmingham-Manchester instead of separate London-Birmingham, London-Manchester and Birmingham-Manchester services, each one at half the frequency that a combined service would have provided). Obviously I understand that, in the real world, there isn't unlimited money and that's why the cheaper (albeit not so good) options tend to be chosen.