1) The input devices are on SPI, not USB. Apple's ACPI tables don't provide the GPIO mappings for these things via the standard mechanisms, so the chipset driver won't bind. You then still need another driver for the SPI controller, and there's an out of tree one at https://github.com/cb22/macbook12-spi-driver/ . Longer term, the kernel needs to be able to parse Apple's ACPI tables and that driver needs merging.
2) Apple's NVME hardware uses the wrong PCI device class, possibly because it's not entirely NVME compatible (trying to read 64 bits of mmio register space in one go will fail, for instance). Linux has a specific entry for the older Apple NVME devices, and that may need to be broadened.
3) Having source ID checking enabled when doing IRQ remapping results in the system hanging on boot. It's unclear what the underlying problem is.
Windows works fine because Apple provide drivers for (1) and (2). (3) is unclear - Windows may be setting up interrupt remapping differently, or it may never enable source ID verification. These issues are far from unusual when dealing with Apple hardware ((1) was true for the new Macbook, (2) has been true since Apple introduced NVME, (3) is the kind of weirdness that we've seen on Apple hardware ever since they went Intel), and this particular set of breakage is unsurprising.
I spend some time while I was at Red Hat trying to keep Apple hardware working (https://mjg59.dreamwidth.org/12037.html is an example of what we had to do), but I don't know that anybody's really working terribly hard on it these days.