I am doing some testing. For some reason I still get crash on 2.8.1.1 sometime.
Crash on startup or crash while playing ? Crash while playing could be an event targetting a province by its id, which would not exist on your map.
Also, the sea province generate by the tool does not seem to respect land mass. I have some sea province split in two unconnected halves by a big land mass.
No it does not, with the "new" method of making sea provinces. It just assigns every pixel of water to the nearest sea zone "node", which is very fast and makes rather nice borders, but usually you have to fix things up a bit by hand around islands and major rivers. In your case it sounds like you could use another sea zone on the other side of your landmass, but it certainly has its quirks.
I also notice that the tool paint all islands without settlement with red color. Do you think it would be better to replace red with black, the designated color for wasteland? The same could be done for unconnected water, like lake, but using white instead.
Maybe that would be best yes, because red isn't recognized by the game. Then again, having a color in provinces.bmp that is not indefinitions.csv does not make the game crash, it just creates a weird "All realm provinces" province. If you get red you should probably fix it manually, though. Usually minor islands are tied to a larger province.
White will never happen with the current method of generating sea zones unless you place absolutely no water nodes on your settlements map.