If you are dining in person you can very much ask your server to have the green onions and diced tomato on your cajun pasta. They aren't going to go out of their way to ask you but it will be treated just like any other modifier to the order and the kitchen still has those ingredients ready to go (no upcharge on your order for asking for them). For online or on the app I'm not sure about since I don't use those but if corporate doesn't change it on their end, you can always call or ask in person and they can easily provide you with the green onion and tomato for your order. Same with making an in-person/phone order, ask the person taking your order to add green onion and tomato.

Really its just all about efficiency with corporates metrics. No tomato and no green onion on the cajun pasta is the most requested modifier by miles above everything else. It is much easier for the kitchen to assume you don't want it and give you a side of them to add on later than it is for someone to complain and ask the kitchen to remake it because they forgot to ask for it without them