The Any% RTA route you're referring to is outdated, but i can explain why you need to steal the fishing rod. The reason is that bombs cannot be purchased or obtained unless you have a bomb bag (did you get your bombs from a chest?). If want to skip getting the bomb bag, you can use RBA to "obtain" it, allowing you to collect/buy bombs. This requires Cojiro RBA.
The new Any% route revolves around an interesting glitch known as Wrong Warping. Basically, if you step into a blue warp at the end of a dungeon while pulling out an ocarina (with the ocarina items glitch), you trigger the blue warp's cutscene, but by having the ocarina out, you can press B to cancel the ocarina mode and be able to walk around. Then, if you change what entrance you're at at the right time (by returning to a farore's wind point, or other things), you end up at a completely different entrance.
The specific method used in any% is the Ganondoor wrong warp, where what you do in the Deku Tree is that after you beat Gohma with a double k.o. jumpslash and return to the boss room, you stand on edge of the blue warp with ocarina items, then maneuver your way to the door you came in from in such a way that when you open the door, you appear on the inner tower collapse scene.