In case someone is looking at this in 2021: This bitmap for indicating where non-zero proofs are needed might not be necessary if your root generation function anyways ingests the leaf index that is supposed to be written and fills up the tree from left to right.
Because I didn’t know, I first ended up implementing the optimization compression proof outlined in the original post of this thread. My commit: Optimizing sparse merkle tree · rugpullindex/indexed-sparse-merkle-tree@dac73bf · GitHub
But then, after looking at the ETH2 deposit contract implementation, I realized that here simply the “size” AKA highest leaf index in the tree is used to determine if a partial proof is a “non-zero” leaf or not: consensus-specs/deposit_contract.sol at 34fc0a5d09fae6649e0c6ac7a0cb09ff5a999957 · ethereum/consensus-specs · GitHub
So I ended up imitating that strategy in my SMT library and also went with using the index parameter to primarily safe gas.
You can find all of the results here: GitHub - rugpullindex/indexed-sparse-merkle-tree