PCIe is an industry standard and it's not tied to Intel. They don't even offer the latest version of PCIe on any of their products currently.
PCIe as a standard is supported on Intel processors and Apples own ARM processors as-well as SPARC, IBM Power, the Open RISCV processors, AMD processors etc
There would be literally no point at all for Apple to abandon it. Similarly Thunderbolt is no longer tied to Apple and third party host chips that support it are coming to market. Apple could integrate Thunderbolt into their own SoC designs going forward.
I get what you're saying regarding that Apple could go fully custom if they wanted but there really is no reason to do that with PCIe it has a very clear and concise roadmap and won't cause them any bottlenecks. The switch away from Intel solves real problems they are having by contrast.
Yeah, it will be interesting to see how this pans out. For the entry level Mac ARM devices, they will probably go with their own ARM CPU+GPU like on iPad so they wont need PCI-E here. The big question is whether they will keep AMD’s GPU in the more powerful solutions because then you’re right they will need to keep PCI, but if AMD’s GPUs are out the door also... well then everything is up in the air.