Ya the roots will grow thru the pot Into the soil. Even in a tent I've had roots come thru pot bottoms. Rocks are heavy but I screen soil and collect the smaller quarter sized ones and use those the bottom of the pot should be as important as the top
Unless your running hydro plastic is as unnatural as you can get for a potting material once u try to understand the science behind growth what you dont see is the most important part of obtaining what you want to see
it's nice to be able to help explain things sometimes