If you look up the history of the temples mentioned in the article, they were more often destroyed by non-religious conflicts, fires, and earthquakes.

My impression is that Japan's temples are regularly destroyed. They're giant wooden structures with zero fire suppression and basically tinder boxes just waiting for a spark. Lo and behold, the Great ____ Earthquake/Fire or war occurs every few hundred years and there she goes.

Ise Jingu in Japan is perhaps the marquee exception, ritually torn down and rebuilt every 20 years in a tradition at least 1300 years old. I think it stands to reason that if ritual reconstruction and maintenance of temple facilities is part of the religious tradition, then temple builders will see regular work.

We shouldn't assume that all of the world's faiths follow the tradition of building temples as permanent monuments of stone and gold.

Aren’t a bunch of Japanese temples already heritage sites?

The big problem with these temples is not religion it’s deforestation. The spine is made of old growth timber. So some of these temples survived over a thousand years until the central pillars were deemed unsound and needed to be replaced. Problem is that the new pillars are estimated to need replacement again in 400 years. They are made of less sturdy stuff.