Late to the party but I'll try to answer some of your questions.
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I'd avoid Asus motherboards for AMD especially since you are looking at an X3D chip. there have been cases of CPUs frying on them. As for your direct question, on AMD the difference in chipsets isn't very big, it usually amounts to more connectors. You can still overclock on both chipsets. AMD chipsets that end in a E indicate that they have PCIe get 5 capabilities.
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While you can go higher than 6000MHz, 6000MHz is the sweetspot for AMD see Igor's lab article on this
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I have no experience in this, so I can't help you
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Onboard heatsink should fine. Speaking of SSDs, you are definitely paying a premium for it since a high-end gen 4 one is a lot cheaper.
Bonus. With such a high-end CPU, I'd consider going with a beefier cooler. I recently built a system with a Ryzen 7900x and a noctua D15. And I am amazed how easily it reaches the thermal limit of 95° celcius in stress tests. I ended up enabling 105w ecomode and while I'm losing 5 percent in performance, I'm also dropping at least 50w in peak power consumption.