Hello jsadoc, and welcome to the forum!
In general an hour is plenty of time to make a connection at any train station in Italy. If trains are late we are generally talking about 15 minutes give or take not an hour late. Milan is laid out like most Italian train stations where the tracks are next to one another and changing trains is as complicated as walking down to the track by number.
That being said the only time I've taken a train from Varenna to Milan it was late - about 40 minutes as I recall - and we missed our connection. Know that if you miss your connection due to the train being late Trenitalia is responsible for re-booking your tickets even if they are not tickets that are subject to change.
Get the Trenitalia app it will allow you to track trains in real time and if your connection has been assigned a track when you arrive you will already know where you are going when you exit the train.
Even given my single experience coming into Milan from Varenna I would still book the later train given all my experiences taking other trains around Italy for whatever that is worth.
Have a great trip,
=Tod