Charging system

Is there anything wrong with combining them so I have one less wire going to the switch? Or would it be better to just leave it as is?
they are separate for a reason, it has to do with back-feeding the starter relay. MATTAX pinpointed the back feed through the ballast resister. ign 2 provides a bypass to the coil and then ign 1 takes over, that means if ign 2 is tied to the starter relay power can back feed from the output of the ballast to the starter relay.

Or would it be better to just leave it as is?
To me that is the best plan. and buying (i know its expensive) premade factory harnesses is the way to go

My plan is to simplify as needed and protect switches that really should be, dump the ammeter, and add in some new circuits for future modifications down the line. Also get rid of the blade connections where possible and use aptiv or just newer connectors in general.
If you really want to "simplify" things you could run all high amperage devices (headlights, parking lights, turn signals, heater motor, etc off their own individual relays like a modern car. It would make tracing out circuits easier GM style Watertight connectors are easy to make up BUT all of your switches and devices will use SAE or blade terminals so then you have a connector going to a pigtail to a connector.