Mallard is right on for determining decking height. The number of inches is not important because all of us are different heights. A shorter person might go as low as 36” while a taller person might go as high as 48” or even more. Some like to view from chest high while others like to view while sitting down. Children and grandchildren can be accommodated with something like a step stool. Those who add a 2nd level or elevated track have to consider that too.
As we age, we also have to think about access from below. If you plan traditional L-girder, note that it adds to the depth of the benchwork. With tabletop style benchwork you have your 1x4 frame topped with plywood/Homasote, so you end up closer to 5” (3.5+.75+.5). However, L-girder adds another 1x4 layer. It has the L-shaped rails for another 4.25”, then the girders, then the plywood/Homasote, around 9” total. That doesn’t sound like much until you’re on your knees crawling underneath to deal with wiring.
I’m not sure what you mean by “holes to fill”, but I’ll assume it’s open style decking. L-girder is just the framing. Like Mallard did, you can still lay plywood on top of it for a full deck. The other option is open cookie-cutter where you just put decking under the tracks and then fill in the open spaces with landscaping. That can be done with plywood/rigid foam panels or other materials to form mountains, etc. Like the track, it’s all supported by the joists or with risers. Here’s a crude example. Note that it has supports for the legs that I didn’t count in the 9” depth, the L-girder rails, the joists and then the full panel decking. In this case it looks like an 8’ section with only 1 center joist vs multiples on 16” centers. If you look at the 2nd photo you’ll see all the parts of benchwork using L-girder as the framing. It shows all the various types of risers, cleats, etc., used to support both open style roadbed and full sheet roadbed. Open style is mostly used where there are a lot of elevation changes throughout the layout. Where that isn’t the case, like yards, full panel is used. When you do open style, you simply cut the section for track out and raise it with risers. You then raise/lower the rest to get the look you want. You can leave it on the joists and fill in with rigid foam and other materials to create rolling hills, etc.
