If you have 11,950,00 / 12,000,000 Gold and your Hall of Fame Bonus + Alliance Bonus would give you up to 100,000 Gold for a battle, the game will say “Limited rewards! Chamber too small” just before you go into battle. In this exmaple you will only be able to gain up to 50,000 Gold because that’s exactly how much more your Chamber can store. To get these 50,000 you have to win the battle with 100%. If you only reach 50%, your reward will be cut in half as usual (25,000 in this case).
The game makes sure that you cannot find any resources in the Vault which you have no storage for. The chests cannot contain any Gold if your Chamber is full at the time when you enter the Vault. They will contain other rewards (such as Ambrosia, Wisdom or Dominance) instead. The only way I can imganine that what you have described could happen is you not getting a battle result of 100% (e.g. by not beating the Gate), thus not gaining the maximum Gold you could get in this battle and therefore having a bit of storage left which makes it possible to find Gold in the Vault which then filled up your storage to the maximum.
Regarding the randomness of the chests in the Vault:
The chances of finding higher rarity rewards increase with the number of chests you open. So if you only open 2 chests (because you didn’t beat the Gate) you will mostly only find lower rarity rewards. The third chest already has a higher chance to contain higher rarity rewards and the last 3 chests have even better chances. It is actually the case that every chest can contain a Godlike reward, it is just very unlikely, especially for the first chests.
TLDR: There is no conspiracy here, simply “the more chests you open the higher your chances of getting better rewards”.
Spending Gems to open all chests in the Vault is actually a really good deal if you are in need of resources, especially when you compare it to buying them directly