Point A is so painfully incorrect, daft and most importantly so frequently used in incorrect arguments the rest is really rather pointless(though largely incorrect also).
The majority of software is written on PCs(or macs/linux with same hardware), you obviously know nothing about it. If I write code for an API that doesn't run on a PC, for hardware not available on PC, to get it to work on a PC regardless of the fact it is written on it, it must be ported. If you don't understand that stop posting on the subject because you are wrong.
Code written on a PC doesn't just automatically work on the hardware it's written on. The majority of AAA titles are designed for consoles with their specific hardware in mind when determining available performance and how to delegate that.
As for games running poorly, you've quite badly ignored the different ways performance can be 'bad'. Watchdogs had significantly more stuttering on the PC version for a huge portion of users than the game had on consoles. You may have been running 60fps vs 30fps on a console, but with varying frame times to a degree it felt less smooth and worse.
Software designed from the ground up to work on a specific architecture generally needs more work than you are suggesting to run efficiently and well. When you know the single hardware configuration things like using timing and frame targets becomes much easier, this is why you get less stuttering. Also DX11 is a huge reason, it's black box and pretty much decides when to batch process a bunch of stuff in an unreliable manor so while on a console you can literally tell it, do this batch of commands now, measure how long it takes and precisely optimise your game to never go over x ms for a specific frame on a PC you can try to tell it to do it but DX11 may decide to delay, do something else first, then run a bunch of crap together causing a delay which leads to a stutter or dropped frames.
DX12 should significantly help with that kind of thing, also getting far higher efficiency out of hardware.
Unified memory on the consoles also helps with reduction in latency and more predictable.
None of your "look it has higher frame rates therefore definitely runs better" comparisons are valid for the reasons above. Watchdogs, AC Unity, in fact most of the games you've mentioned are stuttering messes on the PC and either not, or not as bad on the consoles.