Some of the bacteria you are growing are on the substrate. Although it is not as big a percentage as the bacteria on the filter media, it will set you back a bit when you remove those bacteria. As others have said, unless you are going for fortified substrate material, the substrate is basically just there to anchor things and the specific inert material won't change things much unless it is so fine grained that it interferes with good water circulation. I keep a Walstad type tank and conventional planted tanks. Both use a variety of small gravel / large sand as the top layer but the Walstad uses a fertile layer under the cap of sandy gravel. I would advise a new fish keeper to master keeping healthy fish before complicating things trying to get a natural planted tank, NPT, right. Once established, an NPT is easy maintenance but the initial setup can be a bit of a pain to get a good balance on. An NPT is not a cycled tank at all, it relies completely on the plants to remove impurities, so getting it right to begin with is essential for the fish. These tanks only get 2 or 3 water changes a year and use no artificial fertilizers for plant growth. They do use fairly high lighting intensity and the fertility is provided by the fish food. It has worked for me on one tank and I am in the process of setting up another but it is chancy at best when you are starting out.