Electronic – Location of power supply

The hard drive power connector ("Molex") predates the PC. It was in use already in 1976 and manufactured by Amp (not Molex). The connector was an established standard even before any of the PC, PC/XT, AT or ATX power supplies became into existence.

Hard drives and such are connected to the motherboard via a control bus (IDE, SATA,...) which provides them the necessary resets and commands. It wasn't really necessary to force any changes to the established power connector, because the hard drive is essentially slow to start up and doesn't need to do anything before it receives a reset from the motherboard, although they can spin up the disk if they so choose. And in any case, hard drives were already manufactured without the need for any "power good" signaling from the power supply.

Peripherals can be fitted with their own voltage supervisory circuits, if needed. Also the power supply could be designed to not to provide power to the Molex connector before the +5 volt and +12 volt supplies become stable.

Good ideas.

Remember to have rational size fuses at the supply end of your power cables to protect against fire due to shorts in the walls. Use the thickest wire for the power pair that you can afford and draw through the walls with ease to minimise losses.

You can add a 48->5V converter for your RPi and perhaps a higher power 48->12V converter for your IR illumination if suitable. Such converters are commodity items.

You could use a second Cat6 cable for the power and use two pairs for ground and two pairs for +48V but it will still be less copper than a dedicated pair of the same overall size.

EDIT:
As clarified by Golanz in the comments above the voltage converters should be of the switching type and not simple linear regulators so the current in the 48V link is reduced, a linear regulator would dissipate lots of energy as heat in the regulator and cause totally unnecessary load on the power supply and wiring by the same amount. Finding linear regulators with a 48V input for 5V output would be harder these days anyway and only appropriate for rare analogue applications.