You're right; the commander doesn't count because it isn't inside the deck while playing—so it's always 99 cards in the deck plus the commander—but it is true that it's confusing for those unfamiliar with the format. I'll add a note to list it as "X + commander."
Viewing post in Neo Forge: MTG Commander vs AI comments
You found a real bug! Depending on how a decklist is written (Moxfield, Arena, commander on the first line...), Forge’s list reader could either move a second card into the command zone or count the commander twice, and that’s the “no more than 99 cards” you saw. It’s fixed for the next update: imported precons come out as 99 + commander. Deck lists will also show 100 cards for a Commander deck, and on Android the deck builder says “99 + commander” like on PC. And the AI deck you pick now shows up under the Opponents button. Thanks again!