In T9608#226589, @epriestley wrote:

(T12812 wants custom headers, but the only use case appears to be better covered by T12813.)

The patch above fixes the issue, but as you mention, double newlines are also considered whitespace, which is pretty bad and removes every empty line.
Additionally, \r is also covered by \s, so the patch above creates a new issue that is very similar to mine: the rule LINT_TRAILING_WHITESPACE fixes line endings even when the rule LINT_DOS_NEWLINE is disabled.