Opinion on universal wiring harness

Keep in mind that the cars are wired so they can be assembled on a production line. If you are doing your own “custom” wiring, you don’t need all the connectors. Some folks remove the connectors on the bulkhead, drill them out, and just run the wires through them directly to where they go. Same with some of other connectors.
Was actually curious about the bulk head. Ive seen on here that other people have deleted it and routed the wires somewhere else is there a common place way of doing this or is it better to leave the bulkhead connectors in for ease of servicing the system. Id like to clean up the engine bay too but one problem at a time lol.