Milan's Malpensa Airport to Duomo

Last Supper is not at the Duomo, if that's what you're saying.

Probably not. Assuming you are coming from the US, it take at least an hour or more to clear immigration. Then an hour train ride to Centrale and maybe 30 minutes more if you just miss the train and have to wait for the next one. From a walk across the plaza to the subway and another 15 minutes to the Duomo. From there I do not remember how far the walk is - maybe another 15. By now it is around 11.30 and that assumes your plane is on time and everything clicks. Now what are you doing with your luggage? Schedule it for the afternoon.

You can take the train to Cadorna, which is a short walk to the Piazza Duomo, where most tours leave from. But it does leave open the question of where to put you luggage. Cadorna does not have luggage storage.
So assuming you land on time at 8:30, get your bags and through customs and immigration at 9:30. 15 minute walk to the train station and purchase tickets, get the 9:56 train to Cadorna, arrive at 10:33, allowing you 12 minutes to walk or taxi to the Piazza Duomo. Luggage??
Maybe you can arrange to meet the tour at the church. The tours usually include a walking tour of Milan, including the Duomo, the Vittorio Emmanuele II shopping mall, the Castello Sforza and end after the tour's appointed time at the Chiesa Santa Maria della Grazie for viewing the Last Supper.

I landed in mxp at 840 am and took a train to catch a 1035 train at Milan central station and made it, although I was advised against it.

With that being said, I did not have any checked luggage, there wasn't a huge line at customs/immigration and my flight was not delayed. you might make it with a minute to spare but that's assuming all of the above and that you don't get lost at all.

If you take the Malpensa Express to Milano Centrale station, it's a different line from the one serving Cadorna and departs every half hour, such as 9:13 to arrive at 10:05 or 9:43 to arrive at 10:35. You can leave luggage at the storage office in Centrale station. From Centrale to Duomo is four stops on Metro Line 3 (yellow). Planning to catch the 9:13 train seems unlikely, at least no better than a 50/50 chance.

If you do think about taking that tour at 10:45, I'd pay the extra $120 to upgrade my seat to Premium Economy and sit as close to that exit door as possible. So I'm one of the first few off that plane. And hopefully you are going carry on only and packing light. make sure you are one of the first into the immigration line