I’ve not been to the Dolomites or to Lake Como, and it’s been 5 years since taking a train west from Milan, but I can assure you that the CT area itself will be crowded, and maybe super crowded. This is based on my visit in October 2021, and the report from some friends who were there last month. They couldn’t get on local trains some days, and had to wait for the next one that had space. We saw tons of people, with streets shoulder to shoulder in Vernazza, and a constant stream of hikers coming up and down the main street in Monterosso, and a mob at the rocky “beach” there, too. The main trail between Vernazza and Corniglia was very very busy.
Maybe the train from Milan to CT wouldn’t be super crowded - maybe - but you’ll likely find a lot of people in the CT once you arrive. Again, I can’t speak about the Dolomites or Lake Como, but you might want to consider them, rather than the CT, to potentially miss super crowding.
If you do go to the CT and want to pick up a car there, I’d imagine that La Spezia, a city much larger than any of the 5 towns, would be the place up pick up your car.