There’s good news and bad news:
That was definitely part of the original idea of the water systems! The original Flow Restructure device had all kinds of provisions for leaving lakes alone above a certain size, allowing lakes in particular areas, etc. And the create water device could allow ‘unrealistic’ deviations from a flow structured terrain, that aren’t always that unrealistic – for example, death valley is cut off from the sea but has no lake 
The problem was, it was extremely scale-sensitive and hard to control - at one scale, a particular ridge would be broken by the algorithm and no lake would form. A res 2x higher and it didn’t happen, and the entire area would flood. Things like that.
In the intervening time, I’ve had a couple ideas that I’m pretty sure can solve this problem, which is the good news. The bad news: I’m not due imminently to revisit the water devices – there are a lot of other areas that need another round of attention before returning to water (which was, after al, focused on in the last named release). I don’t know exactly when that will be; but I definitely look forward to it because outside of the ‘leave lakes alone’ mask input, there’s also multithreading support in the pipeline which will dramatically reduce the amount of time these devices take.