* does my motherboard m.2 slot support PCIe or SATA m.2 SSD-s?
* on AMD motherboards: will my CPU work out of the box or do I need a loaner CPU to perform a BIOS update?
* using the wrong fan header on the motherboard for your AIO water cooler
* not setting the proper XMP profile for your RAM
Those are the ones that I could think of immediately.
Definitely SATA, most likely m.2 as well. They're not either/or.
More likely, you'll run into exhausting your PCIe lanes and might knock your GPU into 8x/4x mode or your additional SSD's into the dedicated SATA lanes.
> on AMD motherboards: will my CPU work out of the box or do I need a loaner CPU to perform a BIOS update?
Unless you fall into a very specific set of Motherboards from during the Zen -> Zen+ transition, the answer is no.
> using the wrong fan header on the motherboard for your AIO water cooler
Any header will still work, and it's not catastrophic anyways. Just change it if you got it wrong. Realistically, any modern motherboard will have the CPU fan header marked clearly, as opposed to the chassis headers.
> not setting the proper XMP profile for your RAM
The point of XMP is that you don't have to choose the profile. You just choose "XMP custom" (or however your motherboard manufacturer labels it) in the UEFI settings. If you don't, you'll get standard JEDEC RAM timings, which is hardly going to stop you.
I mean, your off the top of your head examples are all pretty easily solvable and probably wouldn't even be encountered unless you were specifically looking for them anyways. And if you don't configure them, most will Just Work (tm) at default configurations.
This isn't the 90's/00's where you had to match graphics interfaces, FSB timing, RAM sockets/timing, modular vs cabled PSUs, set jumpers, configure components' master/slave relationships, run molex's/splitters, maximize board fans, clump case/button/etc connectors, terminate sockets, etc, etc.