Itinerary including Lake Como, Bruges, Antwerp, Paris

Hi!
The Bernina Railway would be a very long excursion from Milan. If you stay in Bellagio or, better, Varenna, it is quite a bit shorter, but still long.
Also, lake Como does not have quite as much to see and do as the Amalfi coast: 5 nights there would be very leisurely.

Personally, I'd remove one night from Milan and one night from lake Como, and use one of the nights in Bruges, and the other one in Pontresina, Switzerland, so that you can better enjoy the Bernina excursion.
And from Pontresina, I would continue on to Zürich airport and fly from there sometime around 4 PM. That way, you get to see the amazing Albula railway as well as the Bernina.

Your route would then be: Milan (2) - Bellagio (4) - Pontresina (1) - Bruges (3) - Antwerp (2) - Paris (3)

Pontresina to Bruges would be a looooong day, but going from Pontresina to Zürich airport isn't much worse than getting from Lake Como to a Milan airport.

Taxi Milan to Bellagio on Lake Como

Did you look at a mapping site? You could pay more for a metered cab than for one of the internal flights in Europe. If you really can't use trains and ferries, book a private driver who will agree for a fixed fare.

Not sure I would use Milan as the base to take the Bernina Express - that would be an incredibly long day. If you are flying into Milan one day there is plenty
I love Bellagio but 5 nights would be 2 nights too many. 2 or 3 full days is plenty
Unless you have reason to be in Brussels I'd skip it and add those nights to Bruges or Paris.

Milan to Bernina in a day? Oh my...I cannot imagine how to accomplish this in a day. You could possibly drive to Chur in around 3 hours but you would have to leave an Italian rental car in Switzerland and I don't see that happening. Probably 5 hours by bus. Then 4 hours by train to Tirano. Then another 2.5 hours back to Milan. Doable, but brutal.

I find Bellagio great for a day trip but not for a base on Lake Como. Far more/better options in Varenna and not as crowded or expensive.

2 nights Bruges & 2 nights Brussels.

To clarify, we are doing a one-day (12 hour) group excursion on the Bernina Express from Tirano with a pick up in Milan.

Thank you so much for your help!

I don't like Milan enough for 3 days. Have you been to Venice?

I guess early September is OK, but I'd make sure your top targets in the Lake district are open for your visit. (I haven't been there.) The date makes sense in view of how hard it is to book in highest season.

Northwest Belgium is discussed a lot here. You can get A LOT of information from the good search engine, top center. I'll just note that unreserved train travel is so easy that you don't really HAVE to change hotels to see two cities. Many people consider Bruges a "must sleep", but I personally find it okay to daytrip to from Antwerp. Note that Paris is well connected to Antwerp, with non-changeable, non-cancellable advance-discount tickets that save a lot of money. Edit: Brussels can also take you to Paris, but the choice of trains and departure stations can be completely different. May work for you, maybe not. But I prefer Antwerp to Brussels, except for those who need to see the Royal Museums of Fine Arts in Brussels. I have daytripped to Brussels from Antwerp several times.

This is only one of many posts, but it starts to discuss your issues and is very recent:
https://community.ricksteves.com/travel-forum/belgium/bruges-or-brussels-as-our-base

If you have the time and energy, it is very hard to exhaust Antwerp's attractions. For example, there's the first-rate outdoor sculpture garden that's a bit hard to reach on foot, the Sunday-only visit to Lillo, an abandoned village, families picnic-ing by the river on weekends, the foot tunnel under the Schelde, the roof of the MAS museum, Reubens' tomb, Vrijdag market, all kinds of things that many visitors never get to.

You have enough time for three locations, but I question how far it is from Milan to Antwerp. You should look into the air connections before you plan too much more. Note that Ryanair probably doesn't fly to BRU, but to an inconvenient secondary airport for Brussels. If Venice has better connections, I'd choose that in a minute. Would you consider someplace closer, like Cologne or even coastal Germany? I can't recommend Ostend, Belgium as a substitute for the Italian lake district, it's not like that at all.

You definitely don't need a group tour for the Bernina Railway, and again: Milan is too far as a starting point!
If you stay in Varenna instead of Bellagio, it becomes feasible from there - by train, on your own. There might be some work on the tracks north of Varenna, but I am not sure about the September 2022 situation.