My thoughts.

When one runs every wire and harness to keep things neat you also know where every wire/harness is. What it does or does not rub on or go under ect. It make it easier to check and verify every connection. It will also improve air circulation through the case.

My case has many things in it, including 14 fans and I have no problem chasing down a wire or harness if I have a problem. Neatness just makes a system easier to work on, maintain and troubleshoot. Every wire in the case hooks to the power supply and/or the power supply. It only takes one shorted wire to destroy what ever, or a lot of what ever's.

I always start with basic.
1. Proper hardware that work with the other hardware. Install the hardware double checking everything, including the motherboard standoffs.
2. Proper neat running of all wires and harness. Even if I have to change the length of the wires.
3. Never have a strain on any connection. It can cause a poor connection even when the connection looks good.
4. Install wires/harness out of the way of proper case air flow.

To me these are just basics of putting together a system.
To me it's cheaper than buying and swapping parts trying to figure out a problem that is caused by a chaffed wire or harness that I cause by not being careful in the first place.