Seeking info on Venice to Malpensa by train and a charming hotel along the way
That is going to require a change in Milano, at Centrale, where you can get the Malpensa Express.
You are wise not to want to count on rail and other schedules the morning of the flight, and I'd suggest that instead of Brescia or Milan you take a look (use booking.com or equivalent) for something in the Malpensa area with free shuttle. You'll find more than just the airport chains and budget bed-in-a-box offerings there, although there are certainly plenty of those.
A big plus of that is that you are then free of rail schedules altogether; you arrive at Malpensa the evening before, take the hotel's shuttle to the hotel, and then return with it in the morning in time for your flight. Otherwise, you'd have the same issue as you have from Venice.