Do young trees planted slightly deep eventually grow tall to expose root flare?

I planted these young guava and wax jambu fruit trees. I did try to plant them high to expose the root flare, but it sank upon watering. So to expose it, I excavated a bit, but now there's this crater/bowl below ground level that get filled back up anyway when I water. Question is, can I just leave it alone? Do trees drag up their base/root flare as they grow taller so the this current crater eventually won't matter? I really don't want to have to dig and disturb the tree if I don't have to. Thanks!