Do you have proof of this?

Obviously it doesn't explain resolution, but Xbone being the lead doesn't explain it, because it's virtually the same architecture as PS4; you shouldn't have to re-optimize. There's likely a good dose of flat out incompetence involved too, but no conspiracy, just a CPU bound engine performing better on the console with the faster CPU.

As for PC, that's probably just good old fashioned Ubisoft laziness.

The only thing having the same architecture means is that they utilize the same instruction set in their assembly code. It has nothing todo with optimization or rather optimization for hardware.

The reasoning for the engine being "CPU bound" doesn't make any sense, unless its developed for/optimized for the XB1. 

EDIT: Especially since you're first sentence is completely invalidated by the second sentence. If no optimization was needed then performance would be at parity. The engine performs better on the platform with a faster CPU despite having the same architecure hence a contradiction. The architecture being doesn't mean anything with regards to optimization, just the instruction set it uses.

Sony was the company who began the moneyhatting practices, Rol is just being ironic.

There's no contradiction; Xbone has a faster CPU, therefore a CPU-bottlenecked engine runs better on it. Xbone/PS4 are so similar that it shouldn't matter which is the lead platform.

If the difference in CPU is what causes the disparity in performance than the similarity in architecture is completely irrelevant. The fact that a disparity exists means that the similarity is MOOT in its context. Optimization is done because of hardware disparity.
Similar architectures only mean that its easier to port across platforms because of the assembly code. If optimization wasn't neccessary, PC ports from consoles would scale perfectly.

As for why the engine is CPU-bottlenecked, it doesn't make sense if it was developed primarily on PC or PS4. Even on XB1 the only reason CPU would be prioritized would be as a concession to meet its target. Once the XB1 version was done, the PS4 version wouldn't utilize its extra graphics processing power unless optimized for it and would be 10% weaker in the CPU department.

Simply making a CPU-bottlenecked engine, and then putting it on the XB1, doesn't make sense, why would CPU, a last resort since it is the slowest part of any game engine, be prioritized on PC where extra power would be abundant

Architecture is irrelevant, therefore which console was the lead is irrelevant The engine is CPU bound, so the faster CPU wins, simple as that, no need for a Microsoft paycheck or an anti-Sony conspiracy.

Architecture is irrelevant, therefore which console was the lead is irrelevant 

Wrong, Which ever console was the lead has the hardware priority, Architecture only has to do with how the code is developed.

The engine is CPU bound

Why is the engine CPU bound? It does not make sense in any scenario where the XB1 is not the lead. Why does it perform better on the platform with better CPU? Hardware priority. XB1 had the development lead, PS4 runs the game with a 10% slower CPU, which slows down all of the rendering that depends on the process that run on that CPU. 40% GPU power advantage isn't utilized.

That also forgoes the need of anti-sony/pro-microsoft, and it makes a whole lot more sense then the engine just being CPU Bound for no reason whatsoever. Just the very fact that it was ported and not optimized is more than enough to satisfy these outcomes. Considering the marketting focus, its completely likely that XB1 was dev focus as well, especially considering that lateral porting is so much easier compared to last gen.

I should point out I'm not championing Xbox One here; the game runs like shit there as well.
I just don't think it's anything shady, just Ubisoft biting off more than they could chew and half-assing it.

If XB1 was the lead, how come it runs like deep-fried crap there as well?

The engine's CPU bound because of the kind of game they wanted to make. They aimed too high and ended up failing to achieve what they set out to on any platform.