You understood it perfectly, the account tree has the unspent outputs of all transactions. The advantage for me of separating the unspent outputs from the transactions is that the transactions are much larger in size (in this scheme) than the unspent outputs, so there is a considerable saving. The minimum output value was borrowed from Bitcoin and it seems to be working well for them. An interesting variation could be forcing the minimum output value to be a multiple of the transaction fee, for example, if you include a transaction fee of X then all outputs must be at least 3X.
I remember that you wanted to have maintenance fees in Cryptonite to control dust but you were having problems with the actual mechanism of deciding the value, but having the stakeholders voting on it seems to be a good solution. Nxt is going to implement (or has already implemented?) voting by stakeholders. It is probably worth seeing how they do it, maybe it is applicable to Cryptonite.