That extra space can be used for an auto topoff tank, media reactors, dosing tanks etc.
As for the skimmer it's been my experience that generally insump skimmers are better than the equivalent hob
skimmer. Hard to say on this one since I'm not sure what your insump skimmer is. As for the sand, if your baffle is open on the bottom don't add sand. It'll just get sucked into the return pump eventually and cause problems.
I'm not a fan of rock rubble, even more so if you have none and will be breaking up larger rocks to make it. Keep the larger rocks and use them in your dt as needed when you scape your dt.