Bellagio to Malpensa

Personally, I always prefer to be close to our airport of departure the night before we fly. When we flew out of Malpensa a few years back, we did exactly what you're considering: left Bergamo for Milan, spent a good chunk of a day exploring the city, and went to the airport early the next morning. It was a good decision for us, and especially so having experienced a train strike on that same trip.

What time is your flight?

In the case of a strike (which I experienced a couple of years ago) there is also bus service from Milano Centrale which actually costs less than the train, runs more frequently, and almost as fast.

If depends also on the time of your flight. We have used a driver service based in Como.

...there is also bus service from Milano Centrale which actually costs
less than the train, runs more frequently, and almost as fast.

We took that shuttle and it worked well, although there weren't any traffic issues as it was so early in the morning. Anyway, I misread the OP as deciding whether to go from Bellagio to Malpensa on flight day, or from Milan to Malpensa. Ooops!

It's a good opportunity to get a look at Milan unless you don't want to leave Bellagio in the morning.

The "sensible" choice is very much dependent on your flight time.

Without that key bit of info, hard to offer advice.