Do they also require both sides to know when the other is joking?
I honestly can't tell, since I don't know you that well. My point about consistency remains, though; you can't say "this doesn't apply because it's from GO" and then go "but this does because it's listed here in GO."
On the note of my being annoyed by rule breaking in some ways and not others, it's more just for consistency's sake. Plus, with Mad Enhancement in particular, you're forcing people to construct all Berserkers in largely the same way because A-rank ME has roleplaying implications. The rest is just fluff.
I do still think the cost systems are rather overcomplicated, and that's a big thing that's offputting for me. It's hard enough coming up with good, interesting Noble Phantasms, let alone trying to contort them to fit into a complex system that might just wind up making them unusable or useless.
Everything I say is a joke. It's cost me three marriages and countless jobs, but momma didn't raise no quitter.
In reality, its self contained. I'm not going to shoe horn it into canon and some concepts will work completely differently then they do in the real thing (just for one example already released, this Holy Grail war grants all the Masters skills equivalent to Magus). If I get something "wrong" and its not obviously intentional, "correcting" me by pointing out something in any canon source is fine (and I might change it, depending on a thousand different factors and the phase of the moon). The rules themselves were really written before F/Go came out, thus couldn't possibly take the new concepts into account as written.
If someone wants to play a Berserker with a lesser enchantment, they are fine with bringing it up with me so we can do a workaround. The rules aren't gospel, and I have already changed a few of them myself.
The system is fairly over-complicated, but that is mainly an issue with character generation. Once the characters have been made, it is less a problem. You have me and whatever partner you have to help you get through it, along with as much time as you need. We were able to get through it fine last game. The last option on essentially everything is "make your own: costs probably this see GM", and as stated I have already been working to make some unique NPs. If you have a good idea that you can't shoehorn into one of the existing ideas, then talk to me and we can work something out.