Thank you for reporting this. We've had a few other users reporting about this issue and we are working on addressing it.
One possible solution we're looking at is to report code coverage on entire MATLAB statements as opposed to lines. That would ensure that a statement like this -
function_handle_with_wrapping_line_for_isequal = @(x) ~isequal(x, x) || ...
would either be marked as covered or not covered in entirety.
Is that something that you would find useful?