Because explosives do not work for Goron Damage Boosting anymore, you have to use Bubbles during the nighttime to get yourself over the fences blocking access to the Graveyard and Canyon.
By putting together a Ground Jump and a jumpslash, you can get past the fence thanks to the Bubble.
If you have the scarecrow's song, you can hookshot the scarecrow and skip the second barrier. But wait, there's more, you can also do EHS to skip getting the Garo Mask without having to Save & Quit.
Due to the remodeling done to the area, it is not possible to Goron Boost Out of Bounds and seam walk to the Canyon. Instead it is possible to just simply backflip on top of a rock placed close to the wall and target the conveniently placed Feather Statue and save the game. After doing so, quit the game via the Home Menu and you will be in front of it upon resuming the game.
It is also possible to just Goron Pound next to the rock and target the statue from there, but it is frame perfect and somewhat difficult. Managing to pull it off saves a few seconds though.
By triple slash clipping into a boulder, you can get into it. Then you can use the Goron Mask to get onto the boulder and Save & Quit.
It is possible to skip Captain Keeta by Goron Pounding on top of the lantern on top of Dampe's house and then climbing the wall as Zora Link or by doing a Long Jump with a bomb. When there, pull out the Hookshot and get hit by the flames surrounding the chest. Quickly L-Target and shoot the chest and mash the A-Button to open it.
During daytime, you can do a Goron Damage Boost off of the Bad Bats around the area to get on top of the Day 1 Grave. Once on top of it, face the front and check the grave to fall off and hit the loading zone. To access the Day 2 section, you can simply do a Long Jump to the other side.
By climbing up on one of the pillars near the entrance of the graveyard, perform a long jump with Zora to get ontop of the grave and enter it at any time of the day without Captain's Hat.
Goron Pound and clip ontop of the lamp, then buffer an untarget sidehop, on the second frame hold L + Right then you'll clip through the door.
In order to skip the Ice Arrows, you have to Zora Long Jump to the other side of the gap from the small post next to the dock. Once there, Hookshot your way to the top like normal.
You can get inside the Music Box House without getting the Song of Storms and watching the cutscene by doing a Hookshot Clip with a Gibdo. To do that, lure a Gibdo to a wall of the house and then stun it with the Zora Barrier. Quickly take off the Zora Mask and walk away from the Gibdo to avoid targeting it. L-Target the wall, walk towards the Gibdo and then sidehop and let go of the Hookshot right when you hit the ground to clip inside.
You can get into Sakon's Hideout anytime with a setup you perform to clip through the door with a bomb.
By getting to the highest point of the invisible seam and a long jump you can make it to the other side without need the ocean title deed.
By performing Down A as Deku you can use the deku flower without having to get the ocean title deed for the deku scrub seller
The whole Castle of Ikana can be skipped by doing a Gainer on top of the Sun Block as Zora and Ledge Clipping from the wall next to the entrance. From there, tap A to let go and B to hit the wall. You will get recoiled to the unloaded interior area, afterwards navigate to Igos du Ikana's room.
Doing a set of consecutive Mask Jumps as Zora you can clip to the top of the Sun Block and skip going through Beneath the Well or getting Gibdo Mask.
By doing many, many Mask Jumps you can skip using Elegy to cross the large gaps.
Using extended hookshot is the simplest way to climb Stone Tower without Elegy. First hookshot to the second level of the area. Get First Person Glitch, then EHS to the hookshot target that's all the way up in the last level of the area.