From the Terminal,
cd into the root folder containing the files with trailing whitespaces, then run the following command:
find . -not \( -name .git -prune \) -type f -print0 | LANG=C LC_CTYPE=C xargs -0 sed -i '' -E "s/[[:space:]]*$//"
The app added helpful documentation comments to each setting it extracts, but the formatting was a bit off: the empty comment lines had a trailing whitespace.
Trailing whitespaces do not impact the app performance and they are not a source of bugs. Still, they are incredibly irritating and unnecessary.
I couldn't help myself and looked for a way to remove them that didn't involve editing all of the files manually. I found it in this answer, which I tweaked a bit to make it a one liner, as shown above.