While it technically is a “physical release” the game doesn’t come with the physical software, but a download code and a box. This isn’t the first time Japan and Europe get in on physical releases with boxed copies, as seen with Pokémon Gold and Pokémon Silver’s 3DS Virtual Console release back in September.
Japan will once again get several bonus items to come with their packaged version:
Game manual-style stickers
Poster showing all the Johto Region Pokémon and their type affinities.
Pokémon Crystal releases on January 26, 2018 for Nintendo 3DS via eShop.