Won't be arriving in Japan by air. Will arrive by ship at Maizuru but depart by air from KIX.
The ICOCA card will require JPY 2,000 upfront but I should get back JPY 1,780 even if unused (just JPY 220 refund fee) and I return it at KIX when I leave and there's the convenience factor as mentioned. The big draw is the discounted Haruka ticket from Kyoto to KIX is JPY 1,600 instead of ~JPY 3,700 for residents.