nobody is saying CISA designed, or will be auditing ballots. and the "rumor" that they printed ballots with secret watermarks is just that, a rumor.
CISA did fund and pilot arlo in 2019. an open source auditing software for the DHS, who would be the ones to audit ballots.
https://www.cisa.gov/news/2019/11/21/cisa-invests-cutting-edge-election-security-auditing-tool-ahead-2020-elections