The thing is, Lantz, you look at the nasuverse the same way you look at your comic books or at star strek: As a collection of stories with characters told in a world that works this way, but with a world (and by extension wordly mechanics) that are interchangeable: Spiderman doesn't always have web-string cartridges throughout the worlds and can just shoots strings by himself in some, so a nasuverse world where a modern man can enter the throne MUST be possible, because only one guy said it wasn't possible.
Except, as I said, multiple writers, reboots. The reason there is canon accepted by fans and canon not accepted by fans is because of those two factors: multiple writers and multiple reboots.
The nasuverse has no reboots, and has one writer. There're character materials that provide one SORTA retcon, and it is completely inconsequential: Shirou lost his mind and the picture of excalibur was blurry anyway. So the canon that is is the only canon and the canon that will be. There is one writer and his word is law.
Learn to look at different works differently: Nasu's stuff doesn't operate the same way as comic books, or star trek, or star wars. There's no extended universe with a gorillion writers, no shitty reboots, no CS Gotos, there is what there is.
If what there is is somehow dissatisfactory to you, then... well, take the bits you like from the nasuverse. Take the bits you like from other things. Write an original world, with inspiration taken from many things. A world where three wizards CAN throw a dragon's soul into a kid without people asking "Doesn't the body reflect the soul? Wasn't HF all about dat shit? Why ain't he scaly?"
And if you're not going to... tough. Nobody, at all, sees the nasuverse the same way you do, but if you want to keep going with your "personal canon," then go ahead. Just don't be surprised when new people drop in and go wtf.
Because... wtf.