You need to do more internet research on Ypres. I think TripAdvisor Belgium Forum has had some threads on "Ieper" by public transportation. I've never been there. I haven't read the word bicycle in a Belgium post here recently, so you need more work on that as well.
You can't appreciate how good the local trains are in this section of Belgium until you've used them. Most of your plan is very practical. I agree that Oosteende is underwhelming reinforced concrete, but with good seafood. It's also early for the season.
I'm a big fan of Antwerp, and would never spend the night in Brugge. But there are divergent opinions on this, especially in the UK.
Saturday is market day in Mechelen, but it's not a must-see-despite having, long ago, been the third largest city on the continent, after the cloth trade faded. Gent is very nice, but so close to Antwerp that I'd rather stay there. A better town than Mechelen could be Leuven, on the way to the airport.
I wasn't familiar with Baarle Nassau, but Wikipedia doesn't give me any reason to spend a day there. Belgium is filled with magnificent medieval town centers and historic Beguinages. Who cares about a town with a border line through it? (opinion BTW, Lille, France is much more worthwhile! I suspect you're coming from the UK, which means a stop in Lille on the train. Check on Walloon restaurants there, too. I went for the Art Museum.) Just to pick two pretty places near your other choices, Lier and Turnhout are nice half or full-days. There are a few attractions in Antwerp, like Cogels-Osy Lei and the MAS museum where you could spend three hours in each. The main art museum in Antwerp is closed for renovation. I prefer the Leuven Beguinage to the more famous one in Brugge. The Turnhout Beguinage is a small gem, with a significant museum of its own. I haven't been there in years, but I found a senior-center with a modest cafe, inside the beguinage, where I had cake and coffee with the old folks. The most important museum in Turnhout is the museum of playing cards, which is not a joke. It turns out to be a great subject for doctoral dissertations ... Exceptional wood carvings in the Turnhout cathedral, which you will enjoy all alone! (The porter gave me some advice last time I was there!)
Brugge has some famous museums, but they have limited, very specific religious art. I like the idea of going there on Monday, because, say, Antwerp has ten or more very fine museums. And Brussels has some fantastic art, like "The Death of Marat", and whole museum just of Magritte. Even the city history museum in Brussels teaches a lot about the history of the kingdom, and the misadventures of Congo.