Bomb Hovering allows you to scale the Stone Tower without the Elegy of Emptiness. There are 2 gaps that must be hovered across to reach the top. The first takes 10 explosives if you start on the hookshot tower. The second takes 11. After that, one last hover across the final gap to reach Stone Tower Temple, taking 8 explosives if hovering from the tower.
Using megaflip hovers you can lower the first gap to 5 explosives, the second gap to 7, and the third to 4.
A much more explosive conservative way to cross the final Stone Tower gap is using Time Stop. In a speedrun, it is convenient to grab the fairy in the second pot from the right of the owl statue. Step on the far right switch and wait for the block shifting cutscene to end. Turn and face towards the wall with the owl statue and stop time. From here, directional inputs are inverse, find your way to the block, and use c-up to cancel stop time and move to the temple's entrance.
Much like inside the Temple itself, a weirdshot can be used to quickly and easily invert the Temple as well. Preforming a weirdshot with the light arrow right after exiting the dungeon puts your camera OoB right behind the red crystal, allowing you to activate it quickly and proceed.
After exiting Stone Tower Temple, walk to the left and use 2 bomb hovers to cross the small gap. About a backflip's distance away from the wall, line yourself up with the middle of the left most block(the ones that move when you stand on the switches). Sidehop to the right and after about 1 second do a bombchu hover. Shoot a light arrow into the center of the middle block to hit the switch, inverting the tower.
A recoil flip or megaflip can also be used to cross the small gap. In a TAS you can shoot the switch without a chu hover.