(Minor update, but surprisingly Olivia lets you pass the vallumental shrine after the koopas run off, meaning you can go get the shell stones before going to the shrine, saving a little bit of time) (Edit : The pillar that is inactive because of the NBH is skipable with a well timed jump from the highest pillar)
I will try my best to attempt those once I get to those parts, but for now Im looking for theory crafting on chpt1. Don't hold me up to it though, you never now when someone will beat me to it Kappa
Over the next few days or weeks I will be willing to go through TOK again on a new file to test any theory that anyone has. Reply to me with them and I will get back to you when I have attempted them. Please try to keep them in chronological order in terms of the story.
Same with the start of ? island for 100%. You can jump over the gap itself or go around the right for a safer and slower method. There is definitely a lot of these throughout the game.
Edit : All the Not-Bottomless holes are skip-able on ? island by going around them. Although the last 2 are considerably harder compared to the first one.
Good chance these are already known, but in the tunnel after bombette 2.0 (kappa) kms' , when going into the mole area, it is possible to jump from the staircase to the higher up part, removing the part where you have to go around. Found this during casual play-through. Also, in the Ice temple, when approaching the spiral staircase with the two ice spikes throwing snowballs down, the game wants you to use confetti to build a path, although you can go around this on the right side. As I said, probably already known but thought no point in not sharing. If needed, I will get images for them.