Dev Here ^^
Thanks for the nice words. You are right - the tutorial is lacking a clear indication that you throw crates. That is likely something that can properly addressed much later in the development. The plan is that the Waifus have tiny little quests for Poneh, which show the game mechanics. So one quest is to throw a container for the Confectionary Waifu to create whipped cream.
Stardust has a funny dynamic right now. At the first levels it's a bit low. You have enough during mid-game and may lack a bit during late-game. The Stardust is also one of the potential grind mechanics. Some people love grinding and some hate it. That's why there is at stardust factor setting so everybody can finely adjust the difficulty.
But the game still needs a money sink. The most likely time to get one implemented properly is when overhauling the crafting system. It's a bit bland right now and doesn't make good use of stardust and materials. It won't be the needed money sink, but it could make stardust more relevant without introducing too much grind.