Let me address your questions in order.
Doesn't matter. Doesn't matter. If it's one-way use another port. Doesn't matter. Doesn't matter. Doesn't matter. Doesn't matter.
The alternate modes are a bit more of an issue, but in a general case 99% of what you plug into your device can go in any port you like and will just work. In the cases of DP / HDMI modes they are switch passthrough so if your device supports the feature they usually work via every port.
Back to Thunderbolt 3 and 4 we're at doesn't matter doesn't matter, again, and have you ever found a PCIe tunnelling device? If you did (congrats, that's an achievement) then you certainly have researched your device and why you need it extensively.
Now why do I write doesn't matter a lot? Because it practically doesn't. My drive a bit slow because it's in a 20gbps port? Whoop de fucking do. My laptop charging slightly slower because PD negotiated 30W instead of 50W? Whoop de fucking do.
This is only a nightmare if you are forced to be in a position to measurebate over numbers. The reality is most things will just work when you plug them in without any thought. It may not operated in a perfectly ideal scenario, but I happily deal with that issue vs having specific ports for specific things.