From what I can see, if I install a bootlid spoiler, the led light wiring would replace the high stop light on the parcel tray.

Is there any reason why I can just wire up both of them? So have the high stop light on the spoiler and the parcel tray both operating

You can use both.
Just run wires from spoiler to parcel shelf brake light and tap into it.
Ive done the same on my ef ghia and el gli.

That was my plan, just wanted to make sure it was a good idea first

I think it would bother me too much having one sitting there doing nothing