A car on lake Como is not of much use, especially for the parking situation. You might be able to save yourself some money if you don't rent a car for those 4 days. A private transfer is an option, but an even cheaper option is to take public transportation. Two ways to do this. Malpensa Express Train from Milan Malpensa to Milan Centrale then train to Varenna-Esino, then ferry across from Varenna to Bellagio. Another option is Malpensa Express from Malpensa airport to Saronno (an intermediate station on the way to Milan), then train from Saronno to Como Lago (last station). Walk across to ferry and take a relaxing ferry from Como to Bellagio through the gorgeous Como branch of the lake. If you are not up to taking the train/ferry option, then renting the car from the start at the airport, might be the cheaper option, because the private transfer option from Malpensa is at least 250€ and from Bellagio to downtown Milan not much less. So even if you won't use the rental car at the lake and keep it parked at a pay lot at 60€ a day rental, and maybe 20€/day parking, you still save over the private transfers. Be aware that to drive from MXP to Bellagio you will take a portion on the A36 freeway (Autostrada Pedemontana Lombarda) between the junction with the A8 and the Junction with the A9. the A36 a toll freeway but there are no toll booths. They take a photo of your license plate at the entry and exit points. To pay for the toll you go to the website below. You can add the app and register ahead of time:
https://www.pedemontana.com/en
you will need the car license plate to pay, so the payment can be made only after you have the rental car.
The drive from Milan to La Moscadella takes forever and a day. If you decide not to have a car while in Bellagio, instead of going to Milan to pick up the car, I would take the train all the way to Florence, or even to Chiusi or Arezzo, and rent the car in one of those cities. If you select the option of picking up in Arezzo or Chiusi (both closer to La Moscadella), Avis-Budget is conveniently located across their respective stations. If you select Florence, then Sixt or Hertz are the best choices (right at the station). Avis-Budget or Europcar are about 15 min walk from the Florence (Firenze) Santa Maria Novella station.
For Sicily I agree that Cefalu is an easy day trip (1 hr) from Palermo, so no need to split your stay.
There is also the train from the Palermo airport to the city (last stop Palermo Centrale).
If you go in September and want to enjoy the beach you can stay in the Mondello district of Palermo (about 30 min by city bus to the city center).
If all you intend to do is see Palermo and Cefalu, you don't need a car at all. Actually having a car while in Palermo is a nightmare worse than having a car in Manhattan. I would rely on trains and buses. If you want to take day trips to surrounding areas by car (like Segesta, Erice, Zingaro, etc.) then I would stay outside of Palermo. The Mondello district would be better. Be aware that almost the entire city center of Palermo is forbidden to non residents' cars, so you might risk getting a camera enforced fine for entering the restricted area (ZTL or Zona Traffico Limitato).
Trains timetables for anywhere mentioned above are below.
www.trenitalia.com
To rent cars I use this broker:
www.autoeurope.com
www.kemwel.com
(different websites but same company, however check prices and options in both).
Read the following:
https://www.autoeurope.com/italy-ztl-zones/
https://en.wikipedia.org/wiki/Road_signs_in_Italy
And get an International Driving Permit (mandatory to drive in Italy) at the AAA office near you.
https://www.aaa.com/vacation/idpf.html
