Looks like the same as Issue 32917. I presume there are two newlines at the end of the file because there are two newlines following every config section.

IMO this is a minor cosmetic annoyance, just like writing a key with an empty value gets you a trailing space after the equals sign at the end of the line. Not worth changing as a bug fix, and not worth a special option, but maybe okay to change if the code is simple and it doesn't harm compatibility.