Thank you for posting this question!
Most of us on the committee would go with your Example 2 (brailling each line continuously using a runover position when necessary.)
None of use would go with your Example 1, because it requires some pretty complex navigation on the part of the reader.
(One additional suggestion was to consider tweaking Example 2 by forcing a line break after each comma so that every expression from “column 2” starts its own braille line. This may help the reader to navigate the material, especially when trying to revisit parts of it.)
–Kyle