Dug some deeper. It seems there is a little bug in Jantje's plugin.
If I fill in constants (i.e. the correct location) in the platform.txt the environment variable is still created wrong (A.BUILD.VARIANT.PATH = "**/**D:/Arduino...etc). This first slash is incorrect. Should not be there. But since I am ignoring this parameter in the SAM platform.txt file it will at least compile fine without having to change the environment variable every time.
Now the clue is to find where this variable is built up. Seems to be in the Helper file. I'll dig deeper.