For blockchains with permissioned mining, MultiChain uses a completely different scheme to bitcoin's. You can find a description of it starting on page 7 of the original MultiChain White Paper:
The maximum transaction throughput of 500-1000 tx/sec includes the time taken to process individual unconfirmed transactions, as well as transactions in blocks. However we wouldn't recommend using a 3 minute block time at that transaction throughput, because that means each block will contain 90000-180000 transactions, which will 'lock' the node for a longer time while the block is being processed. Is there any reason why you don't want to use 5-10 second blocks instead?