I have the reference client running with a complete transaction index.
Is it possible to get all UTXO for a certain height of the chain either via
bitcoin-cli or some other tool?
The utxo set is indexed by
transaction_id + out_index from Bitcoin Core 0.15 onwards (just by
transaction_id from 0.8 - 0.14). So in order to get all UTXOs for a certain height you need to parse the whole set and filter it by height.
There's no way of doing so with
bitcoin-cli AFAIK. You can do it by using STATUS (a tool I'm coauthor of). Feel free to ask for support if needed.