I have this question too. I have used the debugger and print() to examine what I get from the HomeKit APIs for a Matter device and I'm not convinced I am getting custom clusters. It would be very useful to know if this is possible and if so how to make it work.
If not, it sounds like I would need to commission the device using the Matter Framework rather than HomeKit with my own certificates and if I do that it isn't clear that the device would appear in the Home app. If that were the case I suppose the user could commission the device twice but that would be a terrible user experience.
Thanks in advance for any assistance offered!