jmtucu, I would open a ticket for perhaps adding the getQueryTime() functionality as I'm fairly sure it doesn't exist. It would likely be pretty visible in the API. Microtime is the right way to do it, however, as you have pointed out, it's annoying to wrap every query with it, but more than that, query() itself if I'm not mistaken has quite a bit of additional processing, which means the times reported are not 100% accurate.
Instead of querying the time for the query itself you're getting the query + all the pre and post-processing of Flourish. If you want the exact query time it would be best to have it wrapped around the actual final query call within Flourish.
It would likely be easy enough to add in a fork if this is for a particular project. But, as I said, opening a ticket will likely get it included unless there's some major reason why it doesn't make sense. I'm just not sure it's particularly useful in a number of cases. Outside of benchmarking, what is the reasoning for it?