Thank you for posting a proposed itinerary, which many questioners don't do. It tells us your interests, and that you have done some study about the city. On Antwerp:
Although it's nice to say that you visited Rubens' home, they don't have a "collection" of works by Rubens. But the KMSKA museum (which is not a private home ... ), which has dozens, is still closed for years of renovation. While it's a matter of taste, I prefer different historic mansions for someone with your time pressure. Look into the Van Den Bergh museum, the Rockox (sp.?) House (a patron of Rubens), and the foundling hospital (Maagdenhuis), which have leather wallpaper rooms and maybe more to see than the Rubenshuis. However, Rubenshuis is convenient to the Meir street. But who needs to shop for the same merchandise sold in every major city? I would enter only two buildings on Meir, the Palais (which is almost never open), and the big historic indoor shopping space Stadsfeestzaal. I never ride ferris wheels, they're just tourist magnets. The Steen castle is, AFAIK, closed. But walk around it to read the thanks to the Canadian regiment that liberated the port and the city. The exhibits in it moved to the MAS. Antwerp has many fine museums, and I'm sure at least one more would appeal to you. (Many Monday closures.)
Edit Additions: Many town halls in Flanders are open to tourists only for a single tour (arranged at the T.I.) on Sunday. Otherwise the interiors are for government business only. (Turnhout and maybe Lier are smaller cities where they may still be open to poking around.) Your plan to stay in one place is good, but research busses/trams if you need them to get to the train station each morning. Local rail is very important to daily life in Flanders, and you may find ticket lines during rush hour. A recent report here stated that American chip cards now work in the automated ticket machines, I don't know myself. Note that the bus/tram company (i.e. your stored-value ticket) is the same EXCEPT in Brussels.
Because I don't ride ferris wheels, I would not be caught near the Atomium. There are a lot of lovely smaller church interiors in Brussels, as well as scenic walks. Their art (and other) museums are quite famous if you have time and its not Monday. The Bozar may be open on Monday, I forget. I assume you have to book in advance to enter the Euro Parliament, assuming they are not in session. I don't dispute their importance, but I don't put that high on my tourism list. You didn't mention Galleries Royale (historic indoor mall), the Baker's street restaurants (reported danger of cheating on bills, not recommending you EAT there, just walk and refuse the touts), Coudenberg Palace historic cellars, History Museum (does not pull punches on King Leopold), Square/Park du Petit Sablon
I found the Gravensteen castle (without children) to be a letdown. Maybe you can walk more of the scenic parts of Gent. Probably no boat ride in the winter. Note that there may be some restoration work being done on the "Altarpiece" at St. Bavo's, which is the main reason for going there.
I have no experience with Belgian Christmas Markets, but I have found a lot of imported low-budget stuff sold at year-round flea markets, like Polish-made casual clothing and so on.