I have 9600x Ryzen (about 6-12 months older than yours) and have a couple of your issues (APIC ID and CPPC ones) however they are not causing any noticeable issues. My CPU throttles frequency correctly
I don’t know how different your CPU is (generation wise) but I would have thought the kinks in bios/microcode would have been worked out by AMD/framework by now. I’m on a desktop with MSI motherboard
Xen is supposed to have improved AMD support in 4.21 so hopefully that will get into Qubes soon