My middle is a picky eater (with tree nut allergies, oh joy) and magically enough he is a fan of the meat sauce at Dland (not meatballs, meat sauce aka bolognese style.)
His fave meat sauce is the adult bolognese at Plaza Inn at DL and again the adult bolognese at Wine Country (table service) at DCA a close second. Alien Pizza planet has a plant based bolognese and spaghetti and meatballs if your son can’t tell the difference (also have cheese pizza and good salads for you if you are so inclined.) I really wish mine would accept cut up meatballs as meat sauce!!!
Kids Burgers are are at many/several QS locations (Hungry Bear, Galactic Grill, Red Rose, Carnation Cafe (table service) @ DL, Flo’s, Smokejumpers, Lamplight (table service) @ DCA). Any of the kids menu burgers usually are very accommodating to be served plain. You may need to order in person vs mobile order to make this happen.
Cheese Pizza (as in mozzarella and sauce, not margherita style) at both parks - as mentioned Alien Pizza Planet at DL and Cafe Daisy has a cheese “flop over” we haven’t yet tried but plan to. Boardwalk Pizza at DCA (can also order a whole pizza for the group which is a nice option.) Hearthstone Lounge at the Grand is a great sit down restaurant that has great selection for the rest of your party as well as a plain cheese pizza.
Alas, no nuggets anywhere on property anymore - the Hungry Bear ones were gone last time. Will he accept chicken tenders cut up? They are fairly plentiful as well.
There definitely are enough options that you won’t be eating at the same 2-3 restaurants your entire stay, and if you mix up your places should be plenty of variety for the other members of your party.
EDIT: I just did a search on the Dland site for marinara (missed that in your post, mine won’t touch it,LOL) and it looks like Carthay Circle has a kids marinara with regular pasta and not whole wheat. So there are some nice sit down options for your party as well as QS.