I'm fine with including cards they've used in the Virtual World but ONLY IF they've used them outside of the Virtual World.
"I think thats mostly wrong, they do have a note that explains the reason why that deck has been listed."
Except that for Lady of Faith, Black Illusion Ritual, Premature Burial, & Cyber Jar Yugi has NEVER used them in a duel. (Excluding Cyber Jar's 1 use in the VW when his deck was merged with Kaiba's, but owning=/=including in your deck.)
We never saw him draw or play them. And the note explaining their inclusion in the decklist is:
The scene that note refers to is where we saw those cards in his deck rebuilding is their only appearance as real cards under Yugi's ownership and that scene is the same scene that shows Yugi owning 2 copies of Giant Soldier of Stone.
With so many mistakes, I don't think it's a reliable basis for cards Yugi uses in his deck.
For example, if Yugi did build his deck with those cards, why would he use the Ritual Spell for Relinquished, something he's NEVER used? Thus, if we didn't see cards from that scene used in a duel, we should assume he decided not to include them in his deckbuilding.
Yugi has NEVER played Premature Burial in a duel, nor has he ever played a real Cyber Jar card, nor Lady of Faith, nor a second Giant Soldier of Stone, nor Black Illusion Ritual.
I'd also debate Kaiba's decks being all BEWD centered when several times, he's been shown to try to use alternate strategies. (Mill, virus, XYZ, general dragons, Obelisk, etc.)
Also, regarding Kaiba's briefcases, the Yugioh Wiki has actually listed the cards in the briefcases that are visible in the scene. I'm not saying to include them in his decks unless he's shown to use them, but it's definitely not every card.
And if you're opposed to taking away cards they own but didn't use then give Kaiba his briefcase cards. It seems clear that several of the cards in the episode 85 scene were just things from Yugi's collection he considered for deckbuilding but didn't use.