12 nights Italy in july

I think your plan sounds very sensible. You are avoiding the temptation of trying to cover too much ground. With such a short trip, you wouldn't want to spend a lot of time traveling and changing hotels.

DON'T skip Florence. Its importance in the history and culture of Western civilization just can't be overestimated.
If you decide that you want to see any of the smaller places, you can do a day trip by train or bus. Orvieto from Rome, Siena from Florence, or Padova from Venice spring to mind as possibilities.
In July, Venice will be jammed. Just accept the fact. One thing you might look into is the Brenta canal cruises They do whole and half days, starting, in your case, from Venice. You stop at a couple of Palladian villas. Our guide was very knowledgeable and interesting. We did the whole day, but I think a half would have been sufficient.
You can google to get particulars. There are two companies with very similar offerings. I believe the word, "burciello" is in the name.

Check water levels at the Venice tourist office before committing to a canal cruise. Sometimes the cruise itinerary is adversely affected. And those things are not cheap. Venice is great for wandering the back streets and canals where few tourists venture. If you have had enough canals before your stay ends, you can take an easy day-trip to either Padua or Vicenza.

Your schedule sounds very well thought out. Do not skip Florence. The only thing I would suggest is forget the car rental. You can get from all your cities to the next by train with a lot fewer headaches.

Good plan! Do it all by train and enjoy these three great Italian cities. You are wise to look at the cruise ship schedule and perhaps you can be there for a couple of days when there are not too many cruise ships in port.You can avoid those crowds by going to San Marco as early as possible or after 16:00. Get out to the Laguna islands, roam in Canareggio, and you will avoid many people.