Many don't realize that Viator is a 3rd party consolidator and does not run the tours themselves. On the Viator site you can go to the "Additional Information" section, click on more and see who the tour provider actually is. If I do a tour I try to book directly with the tour provider if they have a website.
As to the Venice in a Day, I'd probably just do the things you have listed on your own.
You'd want to try and get into St Marks about 11A to see the lights turn on the ceiling mosaics. I enjoyed doing the whole nine yards...seeing the small area behind the altar (extra charge) as well as the museum upstairs (extra charge) which are on the combined ticket bought directly from the church's ticketing website. I loved seeing the ancient bronze horse statues up in the museum as well as stepping out onto the balcony for the view of the Square. The horses date from either 2nd-3rd century AD back to possibly 4th-5th century BC.
For the Doges Palace, I did the Secret Itinerary but you can see a lot if you just buy the general admission. Again, I purchased directly thru the Doge ticketing site.
On the gondola, there are a number of gondola "stations" dotted around. If there is not one near your hotel, there is one just off St Mark's Square by the Hard Rock Cafe, lol.
I've not gone out to the islands in my 3 visits to Venice. Too much to see, lol!! BUT you do you!