You can’t book the first part as it is a Regional train without seat booking facilities.

From what I read, if I miss the connection from Milan to Venice, then I lose my booking fee. I have also heard that Italian trains often run late. Is a 25 minute interchange too risky?

You shouldn't. I'd expect Trenitalia to rebook you free of charge.

Timekeeping in Italy is not too bad. Certainly a lot better than currently in Germany...

I’d like to make the following trip but on this web site it says I have to break the trip down into 2 trips because I don’t need to reserve a seat on the first leg. Other sites seem to suggest that I can book the entire journey. My understanding is that if I book the entire journey and the first leg runs late, it’s up to the carrier to help me get a connecting train without penalty. But if I do as this site suggests and break the trip down into two legs and the first train runs late, then I lose my reservation cost on the second leg. Is my understanding correct? Should I book the trip on another site that allows the whole journey to be booked, or would it be safe to break it down? 

 

 

If you have even more time you could do the whole Route Reservation free :) 

Regionaltrain to Milano 
then Regionaltrain Milano - Verona and finally another Regionaltrain Verona - Venice would take longer but you save the reservation fee :) 

Thanks for the suggestion. It looks like the alternative is about an hour and 10 minutes longer, and we can live with that. It also involves catching the same regional train from Varenna to Milan, so we could always wait till we’re almost at Milan and if we’re running on time, we could see if the high speed option is still available, and we want to pay the extra money to save an hour of travel Maybe just sitting back and looking at the scenery might be a better way to go.

2 things :

Italian regional trains do not have 1st class seating. You'll have to sit in 2nd class which is totally fine and allowed, I just wanted to let you know !

The EC (coming from Switzerland) is quite small but I would expect to be a few seats left on the day, an April weekday outside holidays. As you said you've alwaya got the regional option.

Overall I don’t think one hour is going to make a big difference. Hopefully, if I have to travel regional, the view will be interesting enough & help me appreciate more about what life in Italy is like.