I don't know man, only thing I can come up is that it's a different item with different properties or more simply in the material world it doesn't have a practical use so he doesn't have it there
according to the walkthough you drink it before you say goodbye to mom? even if he is able to teleport it into the sin base that would require him moving it into a different dimension anyway (maybe you could argue he used the cracks from hex to send it).You don't drink it in the dream world, Shopkeep teleports it to MC's cell so that he can drink it once he wakes up. On the other hand, Shopkeep can sell you the monster parts regardless of whether you're in the physical world or dream world, so he clearly has some ability to transfer objects between them.
My guess is that Shopkeep didn't sell Henri the rune stone just because he wanted the MC to be the one to use it. Shopkeep seems to want the MC to know about the alt-humans, most of the details we have on them came directly or indirectly from something he sold us. He probably knew Henri would climb the Vestige's tower if he had full lucidity and wanted to make sure the MC was along for it.
I agree with you in story (especially about him hinting to dumb boi MC about alt stuff) but when you consider the "overall game?" it kind of makes him seem dumb/poor planning etc.
for us metagaming every choice slyly siding with MC is a great choice..... but what about all the MC who never bought anything from him and ended up in dead end? shopkeep left with his dick in his hand because he put all his eggs in a basket that regularly admits its stiupid