I just walked over to 3 convenience stores that have a large candy selections. The 7/11 had no Kit Kats out of 80 chocolate based candies on display. There were also non-chocolate based candies as well as other snacks. The 2 Family Marts, one had a single "maple" flavor. The other had a chestnut flavor but similar to the 7/11 those were 1 of 50-90 other chocolate candies.
That said since you're more likely to be a vistor if you're reading this, if you want to go crazy for Kit Kats there's a few of "high end" Kit Kat stands you can bring back more rare $4-$5 per stick Kit Kats (probably mentioned in the article)
https://nestle.jp/brand/kit/inbound/en/chocolatory/store.htm...
You can see examples here
https://nestle.jp/brand/kit/inbound/en/chocolatory/product.h...
or better pictures here