I've replicated your game from your screenshot a bit more in detail and I believe you've missed that you still need to build storage facilities ("Foundation Stockpile", "Technological Depot", "Spiritual Repository", "Stellar Cache") besides the "Dimensional Storage", as the "Dimensional Storage" only multiplies the capacity of the others.
From your storage numbers, it seems that you currently do not have any of those on Noxu-b, nor anywhere else. So currently your dimensional storages are multiplying only the base capacity of 10, instead of the e.g. 200k Flux from the "Foundation Stockpile". If you build one of those, your storage capacity should be more than sufficient. You definitely shouldn't need that many "dimensional storages", around 5 should be good. Please tell me if that resolves your issue!
However, I see that this might not have been communicated well by the game. I've updated it (v1.1.0) and adjusted the wording on the Dimensional Storage. I've also adjusted the ending sequence in general.