If you need to be in Wuhan at a certain day/time, I would book the 90 min connection via HKG as it would be safer, but if being rebook on the next PEK-Wuhan flight does not ruin everything for you (but will still be inconvienient of course) I would book the flights via PEK.

You have a valid connection on one ticket so you should be fine if you miss the PEK-Wuhan flight - but of course if the AMS-PEK flight lands on time, you may have to explain why you missed the Wuhan flight given that MCT was complied with. Obviously, taking a break, "sightseing" or visiting lounges on the way to the gate will not be acceptable excuses.

I agree, the reply in the email is wrong; if you miss the flight due to reasons outside your own control, CZ will have to rebook you free of charge (and to pay for hotel and meals if overnight stay is needed).