I only know of 2 so far, skipping the final boss in Elden Ring with the zip glitch, and in legend of korra, taking hundun's health down instantly in the 2nd part of the battle, to start the 3rd part.

In the Predator campaign of Aliens versus Predator 2, getting precise headshots on the final two bosses results in very quick kills. (timestamped to first of two bosses). The first boss dies in 3-5 headshots, before it even jumps down to the arena you're supposed to fight in, and the final boss dies in 1 nice headshot.

@SioN end credit warps don't count. I mean skips that's actually at the area of the final boss or in the boss fight

Final Fantasy 5 skips the real final boss Neo Exdeath by applying berserk to Exdeath Tree, so his AI skips over the part of his script to summon Neo Exdeath.

I'm not sure if any of these are exactly what you are looking for, but here are some interesting boss 'skips' in games that I run.

Mobility! - If you reset immediately after touching a checkpoint in the final boss, for some reason it registers another hit on the boss and allows you to skip a phase. It can be done on either the second or third phase, and depending on which category you are running it is faster to skip either phase. Here is a video of the skip being done on phase two.

Platformer Game - This is my personal favorite skip simply because of how strange it is. To do the skip, you first push the boss to the right side of the screen. Then, you jump into a wall of lava and land a hit on the boss at the same time as you die. This sends the player back a few levels before the bossfight, and prevents the boss from despawning. If you go fast enough, you can make it back to the boss arena before the boss despawns. Doing so spawns a second boss. The second boss can deal damage to the first boss, and vice versa, so by pushing both of them to the right side of the screen you can get them caught in a loop where they both damage each other immediately, resulting in a 20 second overall timesave. I probably explained that poorly, so here is a video of it being done in a run.

Tim_ - The normal way to beat this boss is to dodge his attacks, and wait until he does an attack where he lowers his hands to try and crush you. You can stand on the back of his hands and ride them up and hit him in the head. You can skip the boss by creating a platform underneath you, and jumping up to the head early. From there, you can stand on the very edge of the hand and jump to stay alive and stay on the hand. Normally, the claws kill you but the very edge of the hand is safe. You can hit him three times this way. It saves roughly a minute from doing the fight normally. Here is a video of the skip. The reason the title says it's only five seconds faster is because there is an alternate way to do the skip that is easier but slower.

Super Blue Boy Planet - In the final boss of this game, you can skip the boss by jumping on the boss and flying through a hole in the ceiling. You can exit the arena and just walk to the end of the level. It is not very hard but is very RNG dependent. Over time, multiple ways of doing the skip have been discovered which allows the skip to be done on most patterns. Here is a video of it.

idk if it counts but in swordigo you can skip the second phase of the bossfight with a weird and precise glitch that makes the boss phase through the floor.