To be honest I think it is all a bit overkill. You can just take the 90 days and extend it, and somewhere half-way, fly to South-Korea and back or take that ferry just as a passenger and back. Could also be worth it if South-Korea is not in your travel plan. The DBS ferry stops at South Korea, but we didn't get of either, because it almost doubles the price if you do Russia-Japan in 2 seperate trips. (and we wouldn't have proper time)
So you can have a few days in Seoul, visit the history museum and some sites, and get back with a new 90 days visa/stamp in Japan.
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2011 Overland from Amsterdam to Nepal and back
2018 Overland from Amsterdam to Tokyo via Central Asia and Mongolia
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