I visited Croatia in early October 2009. The weather turns colder at some point during the month (or perhaps early November - who knows these days?). I had great weather in Dubrovnik but the day I left for Korcula, it turned cold and rainy, and I was told the Buza Bar in Dubrovnik closed for the year as soon as that happened. Obviously the weather differs from year to year. Could still be great while you are there, could be cold and rainy already. You're always playing the odds with the weather. If I were going back in the fall, I'd probably go end of September vs. early October, personally. Some things start to end for the season by October (fewer excursions, shorter hours for places). On the upside, mid-October means fewer crowds.
If I were renting a car in Dubrovnik now (I agree, you don't want/need one while there), I'd simply look for the best rates for a "downtown" location on rental sites like EconomyCarRentals (which I used once), Kemwel, Auto Europe, etc. Then, see where their rental office is vs. where you are planning to stay. Then it's just a matter of getting to the car rental office: by bus, taxi, Uber, whatever. Sometimes they will pick you up or even deliver the car to you wherever you are.
Regarding islands: I only visited Korcula, and I did it without a car. That would be too long of a day trip for me personally, but it wouldn't be so bad to spend a few nights there on the way north. However, the island towns do start slowing down as the season ends in October. Korcula was dead at night the nights I stayed there, but restaurants were open.