The substitute was this season adjusted from being a medical to a tactical change.
Clubs either have to drop a player to their emergencies then name them as the substitute on game day, or pick a substitute who didn't play the previous week.
Essendon made a late change on Sunday against GWS in dropping ex-skipper Dyson Heppell, whose form had been under scrutiny, to substitute in order to bring in ruckman Andrew Phillips.
Scott said Essendon had that call ticked off by the AFL ahead of their 11.22 (88) to 11.9 (75) victory.
"To be perfectly honest, we had a situation where Phillips didn't play last week so we didn't have to name our sub out," Scott said.
"Whereas other teams, if you're going to drop someone or make them the sub, you've got to name them as omitted and we certainly didn't want to do that with Heppell but we felt that Heppell was the right sub for us this week."
Richmond coach Damien Hardwick said it was "farcical" the Tigers had to name eventual substitute Trent Cotchin outside their team against the Western Bulldogs when they always planned to use him, while Kangaroos coach Alastair Clarkson also queried the "unfortunate quirk".
Meanwhile, Geelong coach Chris Scott clarified Ollie Henry was not omitted but would be the substitute against Hawthorn on Monday.
"Yep. It just makes sense (to be able to name 23)," former AFL general manager of football Brad Scott said.
"But having worked at the AFL I know that the lawyers would hate that because they've got to re-write the entire rulebook because the rulebook's written around 22 players.
"So they've got to change a lot of things.
"But at the end of the day, it's doable to change it and I think it's just logical because having to name Trent Cotchin as omitted when he's not omitted just doesn't feel right.
"It just creates unnecessary angst across the board."
Scott said when he was at the AFL the league asked clubs whether they preferred five on the bench or four plus a substitute - with the majority wanting the latter, to his surprise.
Scott praised Heppell's reaction, while stressing he was still "very important" to Essendon despite being subbed off and on in recent weeks.
"He's spoken to the players that they're the rules and we've got to play to them and we want the result for the team and he's led the way there," Scott said.
Scott said Essendon wanted to play rucks Phillips and Sam Draper together and liked the versatility as substitute of Heppell, who replaced Sam Weideman (concussion) in the second quarter.
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