Timeless and Spaced out are countered by Ars Paulina, not the other way around.
None Direction is countered by the Mist screwing over his sense of direction and thus ability to control None Direction, not the other way around.
A++ Luck that warps fate and causality > Favours of the fortunate
Conceptually impaling branches that can be grown from any part of Ruler's body, combined with Eyes of the Mind and SNI telling him the best way to fight with them > Disarmed
Ruler rewrite the world with a law that disallows Hunter's powers and says he cannot exist > Compulsory existence
If Hunter regenerates from a wound that would be lethal to a normal person (e.g. a branch impaling him through the heart) even once while he is in Patchwork Soul, he becomes (re) born of Patchwork Soul, and nothing he can do can affect Ruler, while Ruler can just bypass all of his resistaces and immunities (Colourful, Untouchable, Inhuman Sold, Thoughtless, Physical Lock, etc)
Several of Hunter's counter abilities are things that need to be manually activated, which I doubt he could do before the effect has occured.
Also, I notice Hunter has no resistance to mind manipulation. Just by seeing the branches he'd become terrified and disorientated, and with Ruler's supernatural charisma he could convince Hunter to stop fighting just by talking to him a bit. Also, Nameless Forest would leave him vegetative, even if it can't erase him permanently
Literally everything in Patchwork Soul is the embodiment of a World, and cannot be even scratched by anything short of an Anti-World class ability. It's a conceptual defense in addition to physical power - unless the ability's purpose and concept is centred around destroying planets/worlds, it won't be able to harm Patchwork Soul's environment in any way, even if it would normally have the power to destroy a planet.
And with CCC, Ruler could just write a law into reality that says Hunter cannot use his powers and cannot exist. And if Hunter does somehow regenerate from that, his regenerated body will qualify as "born of patchwork soul" and everything he can do to Ruler will be lolnoped.
As for killing Ruler...
Godhand means that no attack that is not A rank (in terms of Rank, not power) will be able to penetrate Ruler's skin. That means that only Hunter's most high quality attacks will be able to penetrate Ruler's skin. It also means that any attack to penetrate Ruler's skin will never be able to do so again. Andreias Amarantos means that if Hunter or his weapon/attacks is not divine in nature, it won't be able to penetrate his skin, and even if it is divine it needs to be on the level of a true gods divinity, not just a demigod or nature spirit, or else the attack's damage will be reduced. Effectively, Ruler has 2 layers of invulnerability that must be bypassed, and once an attack has bypassed it, that attack will never be able to do so again.
Assuming Absolute Zero gets passed the invulnerability, it will do nothing as Ruler can just create a different body to use. Delete will do nothing, as Ruler could just Enfer Chateau D'lf back in time, or create a new body at any point in space-time anyway, and it won't work on his soul/conciousness because his consciousness is already at all points throughout space-time, including its very end. Ground control turning Ruler into a black hole wouldn't work for the same reasons (not to mention that if it is a real black hole as "control over gravity" would imply, he'd be well above 7-C or even 5-C likely)
Can he (and would he know to) destroy the 4 dimensional construct that is Ruler's soul/mind, that is effectively omnipresent? Its a 4-D construct compared to Threads of Fate, Hallowed Reaping, Hell's Fury and Heaven's Judgment which are all 3-D abilities. Ruler's soul is literally 2 degrees of infinity greater than them. And when Hunter is in Patchwork Soul can he destroy the soul/mind that exists across Space-time, and when he is in space-time can he destroy the soul/mind that exists in Patchwork Soul?
Can he kill every living thing in the infinite worlds of Patchwork Soul? At once? because those worlds are endlessly being created and duplicated at the behest of
Akasha itself? Because Ruler won't die without that happening.
And with God-Father's Authority, within Patchwork Soul, nothing Hunter does that involves using the surrounding environment, or the creation/growth of anything new, can affect Ruler.
Also, Hunters "conquer anything he puts his mind to" and all related abilities, strike me as a form of reality warping and mind manipulation. Ruler is highly resistant to both.
Ruler also freely uses SNI in the middle of battle, so he would know to do all this first thing if he wants to survive, and would not hesitate.