It doesn't have to be a problem
in my case, I made the border at the end of the WIP because I knew I wanted to add "waves" around the coastline. I also had too few place to put the title of my map under the continent so I had to expand it afterwards...
If you don't intend to do so, you will have no problem for this
For the colour of your political regions, if each isle shall be a different region, it is easy to select each one with the magic wand selector in GIMP, when you are on your coastline layer.
I would suggest you to add those colours on a new layer especially created for this task, so you can modify, hide or delete it whenever you want.