I've been doing some looking into this and my admittedly cursory research reveals something odd. Stern's first ever pinball machine was the Harley Davidson in 1999. That machine was made by SEGA originally but was continued by Stern Pinball who continued to produce their own machines until the present day. All their releases from around 2001 are of western properties like Austin Powers and the NFL. The first even vaguely japanese thing Stern has made to date is the Pokémon machine, themed around the 1999 anime. That released last year. Why would they try and make something based on a relatively unknown horror manga author in 2001? Unless someone on the inside was desperate for it to exist I think we're looking at a custom job.

Hi! Indeed, according to this : https://itch.io/t/5889447/ito-documentary-research
the early project was developed by Watanabe (with a first prototype, a mock up machine) then Sega decided to not release the project (so would have Stern as it's really niche as you mentionned) Watanabe would have paid to build 3 machines in China .

To my knowledge ; now we have 4 pinballs, one of them is in japan, at least 2 of them are in the USA (including one that may have been rebranded as an X-men pinball machine), and the last one is still not located !