@freecia
Those are pretty good coverages offered by your car rental agency! Except for that 100k yen deductible for (c).

By declining your included CDW, the only thing you gain is that you save yourself the NOC waiver fee (only 540yen/day) and that you're more likely to be off the hook for any portion of tire repair (which I presume your CC would entirely cover, but I may be wrong) than your Safety Pack option.

By taking the included CDW and then paying for the Safety Pack, you gain the benefit of likely having to deal with less headache (eg, more paperwork, pay upfront then trying to recoup money from your CC) in case you have an incident.

I agree with you that I'd go with the latter option.
(note I did not click on and read over your OTS links)