I'm sort of not clearly understanding everything you're saying.
Looking at your linked page, I will say that their options are rather atypical. A typical situation is that the rental car agency offers one standard insurance coverage terms, with different waiver and road service options (CDW, NOC waiver, roadside service, comprehensive CDW + NOC waiver which may include roadside service and often may also exempt you from responsibility for tire damage). With your agency, what they're offering are two different types of coverage with roadside service and tire repair rolled into the superior coverage plan. Your website does not state how much the superior plan (Recommended course) costs, so you'll have to find that out. Otherwise all the info is there, and I think the wiki gives you most things you need to consider to make the decision. Only you can judge your own comfort level with different risks and how much you value things like roadside service, benefit of CDW by letting the rental car place deal with the damage versus dealing with your credit card company in case of damage to vehicle (Jpn rental car companies are sticklers for having police report for everything, but going through your credit card company will probably necessitate multiple phone calls and paperwork and lining up documentations), etc. As far as roadside service is considered, you'll be entitled to JAF service anyways if you're AAA/CAA member although I only know that on paper and don't know how seamless that is firsthand. One other variable is your credit card... significant difference between what you get from Chase United Club / Sapphire Reserve versus something like AMEx Platinum.