My Way Italy - recent experience?

I would not worry about it--late September into October is a pretty ideal time to plan a trip! If you plan much later, you have risk of inclement weather.
There will be crowds because these are very popular places, but going in the dead of winter has its drawbacks. If you find the crowds detract from your experience, you can plan a trip in the future that takes in "second tier" places--all of the charm, a fraction of the crowds.

Well, we did it in 2022 which may not be as recent as you hoped for, but I will throw in thoughts. We took the tour in mid-May which is a pretty busy time. It’s popular because of the weather and there are school field trips as well. Also, it was really the first big travel year after Covid. Crowds really never impacted us (exception was the Trevi fountain) although we had already seen the major sites, so we weren’t trying to work those in. Getting and early start helped as well as avoiding the crowds during the middle of the day.

For things we really wanted to see, we booked ahead. Venice was perfect early in the day and after the tour groups left- 3-4:00 ish. Varenna was wonderful and the only place we found crowds was Bellagio at lunch time. We did know exactly what ticket we wanted for the ferry on Lake Como, so that purchase was quick and we went early. Cinque Terre (Monterosso) was the only place where we needed dinner reservations to eat where we wanted (Bellvedere) but the hotel manager interceded for us. Our guide made sure we knew what pass to buy for the trains in Cinque Terre so we only had to use the ticket machine once. The afternoons and evenings were lovely and not very crowded in Monterosso. There was a fabulous laundry in Monterosso. No problems with crowds in Assisi. Florence and Rome are busy, popular cities, but as long as you’ve booked what you want to see, the crowds shouldn’t cause problems.

This was a wonderful tour for us - get out early and then use the afternoons and evening as well.