The rules of Side Deck are provided officially by Konami of the Speed Duel format. The Limited 1, Limited 2, and Limited 3 follow the same behavior. Both the main+extra+side combined are counted towards the banlist.
Duel Links is an incomplete simulation of the Speed Duel rules where all duels are singles, without having the option to select chain order or select zones. In Omega, we want to follow the actual rules of Speed Duel.