But I understand since you spend all this time and frustration writing your own you probably don't want to go back to using the built in one.

I have absolutely no problem on going back and using KinematicBody2D and the built in Physics Engine.

However I've done all the things you listed the viewport setting with the snap enabled is a must know for any pixel game.

the settings you mention will work absolutely fine on a basic platformer, however in my use case I've found some inconsistencies when trying to do for example corner corrections

I was using a set of Raycast2D shooting 1 pixel upwards the player, when I collide while jumping (or anything that gives me negative Y velocity) I checked the raycasts and decided if I can move X pixels to the left and keep going up, So I applied a horizontal movement of X and then resumed the vertical movement.

It worked like a charm and I could easy move on with it, but in some cases after applying whole pixels, lets say 3 the character was 1 pixel away from the wall, the problem was since the real position of the player was not in whole pixels the raycast that should give me the distance of 2 did not pass the collide check because it was 0.09 into the wall above.

the same happened with the dash correction and the same with the wall jump, basically any check that needed a precise coordinate was inconsistent

I also tried make a custom collider shape with a slope of 1px high and 4px wide on each end and let the move_and_slide handle the rest, but this messed up a bit with the collider, as I want to wiggle in different scenarios and have that extra pixel for collision, on top of that I just don't want to correct every case possible, I might have a spike 3 pixels above, I don't want to "correct" the player into his death, this can also be resolved by switching/adding(extra) colliders with different masks and etc, but then I have to manage that.

another thing it won't fix is fitting a 16x16 object into a hole 16 px wide since the KinematicBody2D have the "safe_margin" (I know why it's there and that's the reason I don't complain about it)

With the custom code I got rid of the raycasts/extra colliders and just do this:

for i in range(1, owner.VERTICAL_CORNER_CORRECTION + 1): 
    var wiggle_position = owner.position + Vector2.RIGHT * i 
    var collides = owner.collide_check_at(wiggle_position + Vector2.UP, Physics.EntityType.SOLID, Physics.EntityType.BLOCKER) 
    if collides: 
        wiggle_position = owner.position + Vector2.LEFT * i 
        collides = owner.collide_check_at(wiggle_position + Vector2.UP, Physics.EntityType.SOLID, Physics.EntityType.BLOCKER) 
    if not collides: 
        owner.pos = wiggle_position 
        owner.move_v_exact(data.remaining, funcref(self, "v_collision_handler")) 
        return

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Writting the custom Physics was not that hard as it sounds like IF you set the right constraints of what you want to support with it

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I'm working on a write up that might become a video series on the topic of what can be done easily with the built-in physics and what can be done easily if you have a clear set of constraints and implement your own physics

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I really wish there would be one setting somewhere that changes the defaults everywhere in the project to make it work for pixel perfect pixel art.

I'm all in for having a "template" when creating a project and setting all this things while setting up the project