The Manual Points mode will be working in next update of Physical Water Surface that will be released very soon. In this update, the Points variable is public and can be edited manually in Manual Mode.
Concerning the transition between different ocean states, I will implement this but it will take some time to find a good solution. The waves going crazy is exactly the thing that needs to be avoided. I suspect that just gradually changing the wave parameters will not look good. I will do some testing with this and let you know what I find.